Two universities that have had their annual funding cut are asking for allocations to be reviewed, fearing that funding chiefs have made a mistake.
Ten English institutions had their overall teaching, widening participation and research funding reduced in last week's provisional allocations for 2008-09, while 49 others had below-inflation increases.
Those receiving the least generous allocations from the Higher Education Funding Council for England said this week that they remained confident that the impact could be mitigated without serious damage to ambitions or operations.
However, Lancaster and Warwick universities have asked Hefce to review its calculations.
Lancaster had its funding cut by 0.4 per cent, compared with an inflation rate of 2.75 per cent and an average increase of 3.5 per cent per institution.
Paul Wellings, the vice-chancellor, said his institution had lost a total of £900,000 under the Government's policy to stop funding students taking a qualification equivalent to, or lower than, one they already hold (an ELQ). A further £267,000 was cut from Lancaster's widening access funds.
He said: "We, along with Warwick, have a very large part-time cohort, and while we knew we would receive a reduction on ELQ we're surprised by the scale and think there may be an error. We will go back to Hefce to talk about that.
"We're slightly more bothered about the widening participation reduction ... because we think that's double jeopardy. We think the consequence of shifting the ELQ numbers is automatically having a knock-on effect on the way that the widening participation premium has been calculated, as the two things in the formula are interrelated."
The University of Warwick, which received a 0.2 per cent cut, has also asked Hefce to explain its disappointing settlement.
"We're not using the words 'fault' or 'wrong', but we certainly weren't expecting it to drop in percentage terms," a spokesman said.
"If you expect a certain amount of money and don't get it, you would like someone somewhere to give you a reason why."