Conflicting priorities within Whitehall in the run-up to the government's strategic paper on higher education are threatening to produce a logjam in academic salaries that could hamper ministers' expansion plans.

The ?4,000 boost to postdoctoral researchers' stipends promised by the Office of Science and Technology will mean that in theory postdocs would have to take a pay cut to become junior lecturers unless education ministers find more money for academic salaries.

The vanishing pay differential could disrupt the flow of young scientists into academia at a time when universities need to recruit thousands more. The Higher Education Funding Council for England estimated this week that the number of people entering academia would need to rise by up to 60 per cent a year to keep pace with growing student recruitment.

Senior politicians called on the OST and the Department for Education and Skills to work together more closely amid concerns that lack of coordination was hindering efforts to improve scientific career prospects. The minimum pay for postdoc researchers is currently ?18,265, while junior lecturer grades start at ?22,191. Lecturers' unions have failed to secure any guarantee of extra funding for permanent staff salaries.

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Tom Wilson, head of the universities department at Natfhe, said that some institutions, particularly those with funding from the Wellcome Trust and the Medical Research Council, were already paying postdocs and junior staff salaries above the standard level.

Keith Root, former director of finance and central issues at the OST, said:

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"Now that the postdocs are being treated OK, it is a case of finding out what the DFES thinks should be happening further up the scale."

Dr Root said that most postdocs already skipped the lowest posts on the scale when they moved to a permanent position. Paying them more would cause more disruption. "The further you put people up the scale, the more expensive it is to the university. There needs to be a total rethink of the way faculty are paid," he said.

In July, the government's science strategy was issued by the Treasury, the Department of Trade and Industry and the DFES. The science budget was announced at the time, but the DFES has yet to reveal details of its spending review settlement for higher education.

Ian Haines, head of the UK deans of science, said rises in postdoc stipends would have a knock-on effect because lecturing staff in science and technology expect the salary differentials between themselves and postdocs to be maintained.

He questioned whether all universities would be able to afford such demands. "The DFES must recognise the problem and increase its allocations to universities," he said.

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Peter Cotgreave, director of the pressure group Save British Science, said:

"It is pretty clear that the OST understands the pay aspects of the recruitment and retention of good people and is doing something about it. It is also pretty clear that the DFES either doesn't understand that it is an issue or suspects that it will cost a lot of money."

Barry Sheerman, chairman of the House of Commons education select committee, said that better communication between the OST and DFES was vital:"This problem has to be looked at quickly because we need a seamless transition from undergraduate to graduate to postdoc and into their professional careers."

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Ian Gibson, chairman of the House of Commons science and technology select committee, said: "It is time for their heads to be knocked together."

In a joint statement, the OST and DFES denied a lack of joined-up thinking:

"The strategy for higher education is being drawn up in consultation with other departments, including the OST."

In its report on future staffing needs, the funding council says the main problem is one of recruitment rather than retention. If widening participation targets are to be met by 2010, another 17,000 academics are needed as expansion cannot be achieved through further efficiency gains.

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The report's surprise finding is that the widely reported "academic timebomb" of a bulge of older staff nearing retirement does not exist.