Other universities may follow London South Bank University and withhold the nationally negotiated 0.5 per cent pay rise, Times Higher Education has learnt.
One vice-chancellor, speaking anonymously, said he was giving serious consideration to the move but was waiting for the grant letter in March before making a decision.
Like Martin Earwicker, vice-chancellor of London South Bank, he said he would prefer to negotiate pay locally.
A second vice-chancellor said several universities were thinking about adopting local pay negotiations, but would remain in the national bargaining process until the last minute to try to influence the result.
"The outcome of national negotiations will have an impact on any local negotiations," he explained.
Les Ebdon, chairman of the Million+ group of new universities, said: "I don't want to predict the imminent collapse of national bargaining, but there are clear pressures on the system and questions over its long-term future."
Another vice-chancellor observed that universities were not following the private sector by offering short-term pay cuts, reduced hours or sabbaticals instead of redundancies.
"It may be that national bargaining is inhibiting deals of that sort," he said.
Alison Wolf, Sir Roy Griffiths professor of public sector management at King's College London, has argued that universities are "shackled" by national wage settlements.
She told Times Higher Education: "Local negotiations would not solve all of today's problems, which are the result largely of a very badly thought out pay settlement.
"But if the senior staff in a department were willing to take a short-term pay cut to save the job of a junior colleague, they can't - whereas in the private sector, people have been doing exactly that."
The higher education labour market was a "class example" of the effect of central pay settlements, she said, offering "good conditions for permanent staff and rubbish ones for 'peripheral' staff, such as graduate students, who are hired at appalling rates".
At senior levels, where pay is often negotiated individually, greater flexibility has enabled new universities to hire academic "stars" more easily than if the salaries were still fixed, she argued. She said this had "stopped the brain drain to America".
Michael MacNeil, head of higher education at the University and College Union, rejected Professor Wolf's assessment of national bargaining. "Across the sector as jobs are cut, the quality of education is under threat. At a time like this, employers and unions must engage in a national dialogue," he said.
"It is frankly irresponsible for commentators to destabilise further an increasingly strained industrial-relations climate."
He added there was "no evidence" to suggest that pay freezes were prevalent across the private sector as a means to save jobs, and was also dismissive of the link drawn by Professor Wolf between the financial difficulties facing the sector and the pay settlement.
"If she is referring to the last pay settlement of 0.5 per cent, then I'm not sure where she is coming from as that did not even match inflation," he said. The 2008 award only kept pace with inflation, he added.
The Universities and Colleges Employers Association said it was up to universities as "autonomous employers" whether to participate in collective pay negotiations.