A deficit of almost ?10 billion in the sector's main pension fund may force radical changes to secure the scheme's long-term future, industry experts have warned.
The Universities Superannuation Scheme, which covers about 300,000 academics and senior administrators from pre-1992 universities, revealed last week that it had a ?9.8 billion deficit, based on a valuation on 31 March. That compares with the ?2.9 billion announced in last year's triennial valuation, when the USS compared the value of its assets against the liabilities of all the pensions owed.
This means the scheme is only 77 per cent funded - compared with 92 per cent in 2011 and 103 per cent at the previous valuation in 2008.
Record-low yields from UK government bonds have been blamed for the increased deficit, with a 24 per cent rise in liabilities compared with a 4.4 per cent appreciation of assets.
Pension providers are only required to take action based on triennial valuations, but the USS could recommend higher employee or employer contributions this year if trustees are sufficiently concerned about its balance sheet.
The USS final-salary pension scheme was closed to new members in October 2011 when it introduced a career-average pension scheme, as well as higher overall contributions.
Academics within the University and College Union at pre-1992 universities are currently "working to contract" in protest against the new deal, which they say is worse than the pensions of lecturers at post-1992 institutions and schoolteachers.
However, John Ralfe, an independent pensions expert, believes further action by the USS is required.
He said many private sector companies with final-salary pension schemes were in a similar position.
"But they have shareholders saying 'we have to close the scheme to existing members'. I don't hear that from David Willetts [minister for universities and science]," he said.
"If you are making promises you can't keep, you need to stop making them. But it is very unlikely given the politics." He said the "two-tier system" was unfair as the final-salary scheme was "spectacularly more generous than the career-average one" and everyone should be on an improved career-average scheme.
Jim Naismith, professor of chemical biology at the University of St Andrews, who has studied the USS, believed it was wrong to ask employers to pay more to make up the deficit.
"The universities are pretty close to the pain point as they are paying 16 per cent [in pension contributions]," he said. "What employers could do is to close the scheme."
He predicted that the scheme would close within 10 years, with all members moving to a career average, as the current set-up was unsustainable.
However, Michael MacNeil, head of higher education at UCU, said the latest valuation painted a "misleading hypothetical picture" and "it would be wrong to plan based on an annual snapshot of the scheme's health".
He said industrial action would continue as the deal for new entrants "compared poorly to those offered to other workers in the publicly funded sector".
A USS spokesman said its trustees will meet in late September to formally decide its response to the annual funding report.