An influential committee of backbench MPs has criticised the Government for "interfering" unduly in how the seven UK research councils spend their money.
In a wide-ranging report on the research councils' 2007 budget allocations, MPs on the House of Commons Innovation, Universities, Science and Skills Select Committee also highlight the "poor leadership" of the Science and Technology Facilities Council - raising questions about the future of its chief executive, Keith Mason.
The 55-page report says that the first science budget allocations of the new Department for Innovation, Universities and Skills have been "marred by poor decisions, which have turned the Government's PR fanfare into a PR disaster".
It raises concerns that, despite an increase in the overall science budget in the 2007 Comprehensive Spending Review, government spending commitments are not fully covered and there is too much interference with how research councils spend their money.
"Large parts of the budget are tied to cross-council programmes that largely follow a government agenda," says the report. "Consequently ... we have reservations about the influence Government appears to have on the use of the budget and the extent to which the Haldane principle (which prevents the Government micromanaging research council budgets) has been upheld."
DIUS's performance in ensuring that research councils are effective, "without interfering in how they spend their money", has been "below par", it adds.
The report examines allocations to individual research councils including the STFC, which announced programme cuts last year because of an £80 million shortfall.
The MPs conclude that while the STFC's problems are rooted in the size of the 2007 settlement, they have been exacerbated by the STFC's "poorly conceived delivery plan, lamentable communication and poor leadership".
It says there are "serious questions" about the role and performance of the STFC's chief executive. The MPs raise doubts that Professor Mason is the right person to carry through the improvements it recommends.
"Substantial and urgent changes are now needed in the way in which the council is run in order to restore confidence and to give it the leadership it desperately needs," says the report.
The report calls for a moratorium on STFC cuts until the government-commissioned Wakeham Review of physics has reported, and it asks the Government to make a statement on the micromanagement of research council budgets. Physics researchers said they hoped the recommendations would be acted on.
Brian Foster from the University of Oxford said the report was a "bombshell" that had identified the main factors contributing to the STFC's problems. James Stirling, pro vice-chancellor for research at Durham University, said the Government and the research community had been badly let down by the STFC, and what was needed now was a "fresh start".