As an associate professor of anthropology at California State University, Sacramento, Liam Murphy was used to addressing classes such as the one gathered in a borrowed room at a community college near Fort Leavenworth, a US Army base in Kansas.

The 20-odd students on the three-day course in ethnographic theory were not, however, university undergraduates. They were a group assembled by the US military. And they were paying rapt attention. "It's rare that I have such an interested and, frankly, quite motivated audience," Murphy says.

The enlisted men and women, non-commissioned officers, diplomats, Iraqi expatriates and civilian social scientists in Murphy's class were training to join five-member Human Terrain Teams embedded with frontline brigades and regimental staff in Iraq and Afghanistan to better understand the social, cultural, economic and political make-up of the places in which the US military operates.

"This is supposed to be a civilian-military hybrid, a case where civilian social scientists and the military work together," Murphy says.

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But for increasing numbers of critics of the Human Terrain Teams, and other post-9/11 programmes for which US government agencies have been recruiting social scientists, this hybridisation is problematic.

Even though these initiatives could be seen as a move to remedy the lack of knowledge often displayed in the past by American troops and officials operating abroad, critics say the secrecy intrinsic to the military and intelligence agencies contradicts the openness expected in social science. They say interviewing subjects while wearing a uniform or carrying a gun, as Human Terrain Team members do, also contravenes a core requirement of research: that its subjects give their free and informed consent. And they complain that the resulting information might be misused.

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According to Rob Albro, an assistant professor of international communication at American University in Washington DC, the Human Terrain Teams idea, "in its barest outline, involves social scientists, typically in uniform, often armed, engaging directly with civilian populations and providing information for brigade-level commanders".

Albro, who also chairs the American Anthropological Association's ad hoc Commission on the Engagement of Anthropology with the US Security and Intelligence Communities, continues: "There's no way you can ensure free and informed consent at the end of a weapon. There's no way you can ensure that the information you collect won't later be used to target populations. This is not what social scientists should be doing."

The complaints echo those made during the Vietnam War, and they have similarly resulted in calls for changes to professional codes of conduct for anthropologists and psychologists. One change is to be discussed this month by members of the American Anthropological Association and another has been passed by the American Psychological Association (APA) for implementation in the summer - sooner, if some members have their way.

But the military has also changed the way it involves social scientists, in part as a result of past problems. It has brought in the civilian National Science Foundation to help it choose which research grants to fund. And it has promised to make the resulting research findings available to anyone who wants to see them, partly by adding them to an existing database at Yale University.

Backers of the Human Terrain Teams and other efforts involving social scientists say they are part of an admirable effort by the Defence Secretary, Robert Gates (who will stay on in Barack Obama's Administration), to boost the military's intellectual capabilities.

They say the protests reflect a longstanding elitism and anti-militarism on the part of ivory-tower academics rather than legitimate conflicts of interest. And the Consortium of Social Science Associations, representing economists, political scientists, linguists, historians, geographers, criminologists and others, is in favour of the military expanding its efforts in the social, behavioural and economic sciences.

"I don't disagree with the critics who argue that anthropology has a chequered history in its relationship with the military, to say the least," says Murphy. "I just believe that it can have more of an impact from inside this programme than from outside. Their conclusion is that this is inevitable, that whenever this kind of thing happens, it's destined to go down a sordid path that will lead to all kinds of terrible things. The conclusion I've drawn is very different. These issues are going to come up over and over again. It's in the best interest of anthropology and the other social sciences to get it right."

But David Price, a professor of anthropology at Saint Martin's University in Washington State, says it is the military that has yet to get things right. "Embedding ethnographers in a battlefield setting flies in the face of basic ethical codes involving the study of human beings, specifically getting meaningful voluntary informed consent."

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Price, who has written a book about US anthropologists who served as advisers during the Second World War, says: "There were some really interesting cultural programmes where anthropologists would embed with troops as they went to theatres in Burma and in China. An anthropologist would get on a transport ship in San Diego with a battalion and so you'd have this long sea voyage where there was this intensive training going on. Officers and enlisted men were given important information about how not to be stupid in another culture. That's very different from what's going on here."

Anthropologists today are involved not only in training Human Terrain Teams, they also serve with them in the field. Dave Matsuda, a 51-year-old professor at California State University, East Bay, for example, went to Baghdad attached to the 82nd Airborne Division's 2nd Brigade Combat Team, helping soldiers to understand the complicated interconnectedness of Iraqi families, clans, political parties and freelance militias.

Critics, Matsuda told a military newspaper, complain that "anthropology can't be part of the Army without being corrupted". But while some of these concerns were legitimate, he said, others resulted from kneejerk anti-militarism, and the stakes were too high for anthropologists not to help.

He gave an example of how US soldiers thought they had resolved a conflict with villagers by making a condolence payment to the family of a man who had been killed. When they returned a few days later, they were attacked because the payment hadn't been accompanied by a ritual of reconciliation. Matsuda said his role was to help avoid such misunderstandings. "I don't want those guys going into that village thinking they have got it all taken care of and they end up getting shot. I want everyone to come home."

An educated and "culturally agile" military "will kill fewer, rather than more, innocent civilians", says Felix Moos, a professor of anthropology at the University of Kansas who has trained Human Terrain Team members. "The discipline of anthropology, at least in the US, is in danger of becoming irrelevant since few if any anthropologists are involved in the governmental or military decision-making processes that really count. Anthropologists should become more involved rather than isolating themselves from the realities," he says.

Albro says that while social scientists can provide guidance from the rear, they shouldn't be on the front lines. "You can't have anthropologists as professional practitioners co-operating in military operations.

"You can have a professional anthropological presence, and we do - there's a fairly healthy community of anthropologists in North America and elsewhere who have Iraq and Afghanistan at the centre of their work. But in the field of conflict? No."

Enlisting social scientists to study strategic issues at arm's length is the idea behind another Pentagon programme, the Minerva Consortium, named after the Roman goddess of wisdom and announced by Gates in April 2008 at a conference of the Association of American Universities. "Too many mistakes have been made over the years because our Government and military did not understand, or even seek to understand, the countries or cultures we were dealing with."

Controversy followed this plan, too - in part because of the amount of money Minerva promised to make available to scholars to study prescribed topics including the Chinese military and technology, cultural change in the Islamic world, and the link between terrorism and religious fundamentalism.

An organisation calling itself the Network of Concerned Anthropologists cautioned that the $50 million (?33.8 million) in research grants flooding into universities from Minerva would cause them to shift from a "focus on issues of utility to war-making". The American Anthropological Association also raised objections. And the military, to the surprise of its critics, agreed to use the National Science Foundation to consider which research to fund.

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Minerva seems different from previous initiatives, says Albro. "The managers of Minerva are hyper-conscious of the ways in which social scientists tend to be disinclined to work with the military. It's not about classified research. It's about basic research. It's not about immediate operational needs. It's about ten years out, 20 years out."

At least two other US government programmes have raised the ire of some academics. The Iraqi Perspectives Project is using experts to review documents removed from Iraqi government offices by the American military. And the Pat Roberts Intelligence Community Scholars Programme, named after a former chairman of the Senate Intelligence Committee, gives graduate students up to $50,000 over two years towards their studies in exchange for serving in an intelligence agency for at least 18 months - without their professors or research subjects knowing the source of their funding.

The Pentagon also spends $44 million a year on scholarships for students who study science and foreign languages and who agree to work for the military after graduation, although this programme is not secret.

"Anyone not declaring who they're working for is a problem in any community, but especially in a community of scholars where openness and honesty is important," Price says.

These issues come down to money, many of the critics concede. In all, the US military hands out $1.56 billion a year for basic research, 60 per cent of it to universities. In an era that has seen a decline in grant funding and fewer jobs for graduates of social-science programmes, the military's largesse is bound to have an impact on their fields.

Like the intelligence community's $50,000 scholarships, the Pentagon's $50 million Minerva research budget "is the underlying dynamic that's going to make it very easy for the military to co-opt anthropology", says Price. "What this does in an economy of scarcity is that it creates areas of interest that people will then try to make their projects. So the Defence Department is basically driving research priorities."

The American Anthropological Association has responded by proposing to change its code of ethics, adopted during the Vietnam War, to require that association members be "honest and transparent" about their research. The full membership is currently voting on this proposal, but consensus is by no means assured.

Here, too, economic expediency plays a role, and has exposed a larger rift. The idea of a blanket ban on secrecy was beaten back because increasing numbers of the association's 11,000 members no longer work in academia, where appointments are scarce. Instead, they have taken jobs not only with the Government but also in the private sector - as consultants, behaviourists, market researchers - where secrecy often is required of them.

Albro says: "There are going to be people who don't care, and they might have really compelling reasons. They owe $90,000 in student loans and this is the only job offer they have. It's a kind of festering disciplinary problem, and that is the continued fault-line between what we might call academic and applied practitioners. It is something that has been building up - the changing demographics of the discipline, the lack of job opportunities in the academy and the increasing numbers of people who are going elsewhere for employment. And the Government is one of those employers."

Even if it is passed, the resolution will not be binding. Albro, who was instrumental in preparing it, says, "It's an aspirational document. You can't forbid people to practise if they violate ethical codes."

But the APA can. It passed a resolution in September banning its 148,000 members from working (or even providing healthcare) in detention facilities that violate international law or the US Constitution. The resolution is due to become official this summer, but some members want it to take effect earlier. Violating the rule will mean being stripped of membership, which is required to practise psychology in the US.

"This is not an anti-military resolution," says Brad Olson, a professor in the School of Education and Social Policy at Northwestern University in Illinois. He is one of the resolution's co-authors and is also on the committee working out its implementation.

"It's not saying that people shouldn't be in the military. It's saying that when we have situations such as Guantanamo Bay or CIA black sites where people are being kidnapped, psychologists cannot contribute to that."

The APA agreement was not passed unanimously. "A great number of people voted against the referendum," Olson says. "A lot of people are very focused on guild issues, and (they think that) once we can tell them they can't be in one place, then we're going to tell them they can't go into, for example, US prisons."

For its part, the military says it simply wants to be more sensitive to the people in the increasingly far-flung places it is being sent.

"The US military has not always made the necessary effort to understand the foreign cultures and societies in which it intended to conduct military operations," concedes the unclassified handbook of the Human Terrain Teams. "As a result, it has not always done a good job of dealing with the cultural environment within which it eventually found itself."

Major-General Benjamin Freakley, commander of the Army's 10th Mountain Division, currently in Afghanistan, has said: "Cultural awareness will not necessarily always enable us to predict what the enemy and non-combatants will do, but it will help us better understand what motivates them, what is important to the host nation in which we serve, and how we can either elicit the support of the population or at least diminish their support and aid to the enemy."

Albro says that although he doesn't object to making the military better understand the world, "some of my colleagues do not support that (objective)". He explains: "They don't want a culturally smarter military. They think that would just make it more effective at doing its job, which is to kill people."

Those anthropologists should take their objections to the ballot box, says Moos. "Such critical individuals should stand for political office rather than be, or become, largely irrelevant critics."

Murphy, who teaches Human Terrain Team members in the Kansas classroom, adds: "Although I can appreciate the argument that we participate or collude in imperialism, I think once you start talking in that way you've begun to moralise. And I don't personally think of anthropology as a religion in that sense. There is more than a little bit of veiled elitism in this, a sort of disciplinary snobbery that, to be an honourable anthropologist, you have to work in academia.

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"This is a case where they feel they can criticise any type of applied work because in this case it's the Army, so it's easy to criticise. There's a sense that only we in academia can preserve our independence of thought, that we exist on a sort of loftier plateau."