Data compiled by financial services firm Mercer found that the schemes at 36 pre-1992 universities had assets worth £4 billion against liabilities of £5.1 billion.
The smallest scheme in the survey has assets of just £6 million and a deficit of less than £1 million, while the largest had assets of £360 million with a deficit of more than £200 million.
The study, based on university balance sheets on 31 July last year, also showed major differences in calculating pension liabilities.
Some universities assumed men would live until the age of 82, while others estimated their average life expectancy at 89.
"A seven-year gap between the shortest and longest life expectancy for employees working in similar roles in the same sector is a bit higher than we'd expect," said Mike Harrison, principal in Mercer's higher education pensions group.
Different schemes also made different assumptions about future levels of inflation. Some put the difference between retail price index increases (the old measure used to determine pension increases in higher education) and consumer price index rises (the new measure, typically lower) at 0.5 per cent a year, while others calculated it at 1 per cent.
Salary growth projections also varied, with some universities budgeting for no pay increase and others assuming a 1.5 per cent rise - despite the existence of national pay bargaining. Meanwhile, some pensions had all their assets in stocks, shares and other growth assets, while others put at least half into less risky, lower-yield government gilts.
Investments are likely to outperform gilts and corporate bonds in the long term, but these assets have been on a "roller-coaster ride" in recent years, added Mr Harrison.
"There is nothing wrong at all with being either at the most cautious or the least cautious edge of the spectrum," he said. "But if you are out on one edge of the spectrum and you do not know why you are there, you should be having a conversation about it."