In the summer of 2008, I was asked by the World Bank to conduct a review of governance arrangements in the Palestinian ÖйúAƬ system. Despite my initial reluctance, I am glad I did. Considering the problems they face, Palestinian society as a whole and its university system in particular are coping remarkably well.

Much about the Palestinian ÖйúAƬ system, and its governance, is admirable. Of Palestine's 13 universities, only two are state-run institutions, reflecting the long period during which the country had no government of its own. The rest are run by charities and other not-for-profit or non-governmental organisations from a variety of backgrounds.

Hebron Polytechnic University, for example, was established by a group of wealthy citizens to enhance the prosperity of their town; Bethlehem University was set up by the Jesuits, although it is largely secular and its student body is almost entirely Muslim. As a consequence, universities in Palestine have a surprising amount of autonomy.

Another positive of the system is that significant numbers of the Palestinian diaspora return with knowledge and expertise, sometimes in retirement - it seems extraordinary that people would choose to return to this troubled area, but they do. And the extensive international goodwill towards Palestine is striking - goodwill difficult to demonstrate in material terms because of the situation on the ground, but nevertheless apparent.

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What I also found, and this was reflected in my study, was that most of the elements required for good governance exist, and to a greater extent than in many other countries where I have conducted similar studies. For example, Palestine's universities have trustees, the funding body is not part of the Government and the quality assurance agency is independent of both.

But among the many problems the system faces, among the most tragic is the self-inflicted wound of the strife between Hamas and Fatah. This effectively means that universities in the West Bank and those in Gaza are run separately. Although academic staff co-operate with each other, there is no co-operation between the systems.

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But the self-inflicted wounds are nothing compared with the problems Palestinians face because of the occupation. Until it is witnessed first hand, it is impossible to imagine what it is like to live under it. Nothing happens in the occupied territories unless the Israelis permit it - as a result, things often do not happen at all.

The most visible and troublesome impediments to most residents are the checkpoints. I am not qualified to judge whether they are effective in terms of their stated purpose of providing security, but they certainly have the effect of humiliating the local population and making everyday life very difficult.

The way the checkpoints are operated and their consequent effect is random and unpredictable. I say this advisedly. On several occasions I witnessed a soldier passing a car through and then walking off to chat to a colleague - once for long enough to smoke a cigarette - before returning to deal with the next. They appear designed to maximise, not minimise, inconvenience and delay. There are fixed checkpoints and flying checkpoints, and both are (presumably deliberately) haphazard and unpredictable. Sometimes they take no time to get through but other times they are closed, meaning that onward travel is impossible.

Some checkpoints are predictably difficult: Nablus is a case in point. I went twice to An-Najah National University in Nablus and each time the checkpoint was crowded, with throngs trying to pass through in both directions. The first time, I was in a car that got through quite quickly. The second time (without explanation - you don't argue or ask for explanations), we were forced to abandon our car, walk through and get a taxi to the university. My companion was a senior and highly respected professor, and for us this was irritating and inconvenient. For young people, especially but not exclusively young men, the checkpoints can be hazardous, and being singled out for extra scrutiny is always a risk. Again, this may be logical to the Israeli security services, but the results as far as universities and students are concerned are very serious and make life extremely difficult.

Students who live outside the city can spend three hours getting to college every day: they arrive late, have to leave early and sometimes may not arrive at all. It is almost impossible for students to study at a university outside their immediate location, meaning that choices for young people are limited to what the local university happens to offer. For example, you can forget about studying medicine unless you happen to live in Jerusalem or Nablus.

It is not just the checkpoints; travel generally is more difficult. One immediate and shocking fact is that Palestinians themselves are forbidden from many of the most direct and best roads between Palestinian towns - only Israelis may use them, so effectively there are separate roads for Israelis and Palestinians. Although that is shocking, it is not a major concern for universities. But the more general constraints on free travel mean that the normal associations between institutions - guest lectures, joint courses, external examining - are impossible. Things such as quality assurance activity take much longer to organise and often have to be conducted without a full complement of people.

My own experience entering the country for the first time offers an indication of the difficulties. As the occupying power, Israel controls who enters and leaves. Although I was not passing through Israel, the very stringent security was perhaps understandable, although I was naively surprised that the fact I was going to Palestine at the request of the World Bank appeared to increase rather than diminish the scrutiny.

What I had not allowed for was the two-and-a-half hours it took to be allowed in, which meant that I arrived for my first meeting after it was due to have ended. The reaction of my Palestinian hosts was one of a complete lack of surprise. It is entirely expected that a meeting bringing people together from different locations will need to proceed with one or more absentees. They do not even blame the Israelis for this. It is just how life is. At least I got in.

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One of the most pressing problems facing universities is that they cannot be certain that any of the overseas appointments they make will be allowed to enter the country by the Israelis. This is a particular issue for staff of Palestinian origin coming from abroad. Some get through and some don't, but the process seems haphazard and the results can be serious. While at An-Najah, I learnt that its nursing department came close to closure when the dean, who is a Palestinian holding Swedish citizenship, was forbidden re-entry after going abroad for a short period.

The Israeli Army is an occupying force and has been for 40 years. This is not a rhetorical statement - that is its legal status in international law, which the Israeli Court of Justice recognises. Given that status, what is reasonable and unreasonable behaviour changes, and I make no comment about that. But I observe that as a result, the army makes periodic incursions into university campuses. Some years ago an entire cohort of students was prevented from graduating when Birzeit University was shut. And there is a constant risk of arrest or worse at the hands of soldiers.

Just as the British Army in Northern Ireland (and indeed the security services today) found that arresting people without trial aided its counter-insurgency efforts, although innocents inevitably suffered, so it is in Palestine. At any point Israeli jails will hold Palestinian students and academics without charge or trial, although no official records are available, and I received no reply from the Israeli Embassy in London to an inquiry I made about the subject. But a professor whose son has recently been released counted 82 students in Israeli jails from Birzeit University alone (it is not known how many of these were held without trial); in 2007, An-Najah estimated that 100 students and six staff were in administrative detention.

I was unable to visit Gaza. My Palestinian assignment came well before the recent Israeli invasion, but even then the World Bank regarded it as risky territory. Needless to say, all the observations I have made about the West Bank apply more keenly to universities in Gaza, which are even more isolated.

The Israeli invasion appears to have targeted them particularly: for example, the engineering department in the Islamic University of Gaza was destroyed. Given Israeli sanctions, it is not known when, or even if, engineering will be a subject that can be offered to students in Gaza again. Because of travel restrictions, students who have begun courses will be unable to complete them, and young Gazans wishing to study engineering will be unable to do so in future.

There has been debate in this country and elsewhere about an academic boycott of Israel, a debate I have not joined. I was struck though by the irony that Israel effectively imposes an academic boycott on Palestinian universities in which the rest of the world participates reluctantly and by proxy.

I have already mentioned the extreme difficulty that foreigners have in coming to work in Palestinian universities; the boycott is not complete, however, and there are some who make it. It has had a predictable and presumably deliberate impact on the equipment and facilities available in Palestine's academy. Nothing enters the country without Israel's approval, which very often is not forthcoming, particularly the import of scientific or engineering equipment.

Some of the refusals are bizarre and random - the Polytechnic University in Hebron, for example, was refused permission to import computer firewall software. Much of the equipment in engineering and science departments is therefore old and cannibalised, and so has a Heath Robinson feel. The Palestinians pride themselves on their resourcefulness in making do and mending, but from an educational point of view it is very unsatisfactory.

Why is all this important? Because education is a way of advancement and escape. That is why there is a strong suspicion among Palestinians that education in general and ÖйúAƬ in particular has been targeted by Israel. There is no particular reason to think that this is true, but it would make sense if it were.

Two things remain with me. First, there have been several generations of Palestinians who have been severely disadvantaged and unable to fulfil their potential because of the conditions under which ÖйúAƬ there has to operate. And second, I am struck by the extraordinary determination of those involved in the Palestinian academy - students, academic staff, administrators - to make the system work. Against all the odds, Palestine has a functioning ÖйúAƬ system that is doing its best for its young people, and that best is remarkably good in the circumstances.

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Bahram Bekhradnia is director of the ÖйúAƬ Policy Institute.