Many senior academic staff are in the dark about how their pay increases are awarded, according to lecturers' union Natfhe.
It has blamed the scrapping of nationally negotiated scales for uncertainties about performance-related pay and the fragmentation of salary arrangements.
A telephone survey of staff above principal lecturer grade at new universities found that two of them, Luton and Staffordshire, pay scales for heads of department at less than the last nationally negotiated minimum of Pounds 26,304. Three other universities - Liverpool John Moores, Middlesex and Plymouth - imposed pay settlements without individual or collective consultation.
Liverpool John Moores denied that senior academic pay was determined arbitrarily, and said there were several opportunities for discussion during the settlement procedure.
"The individualising of pay arrangements in the new universities is not generally regarded as satisfactory or fair," said David Farnham, professor of employment relations at Portsmouth University and survey organiser.
"Most appeared concerned at the secrecy surrounding pay levels and pay increases," he said.
The findings were based on interviews with heads of department - deans, associate deans, professors and programme directors - at 30 new universities. Their salaries ranged from Pounds 24,300 to Pounds 50,000, with six institutions paying salaries on incremental scales and 18 paying spot salaries within specified bands.
There were performance-related pay schemes at 22, although respondents were unclear as to who received them and the criteria for allocation.
Collective bargaining was still used for determining pay settlements in 16, while in 11 more there was individual consultation.