The Commons science and technology committee has raised concerns that European funding might distort the UK's research agenda.
During a session on UK science and Europe, committee members said too few policy-makers set the priorities for the huge Framework 6 programme budget.
They were also worried that UK researchers might change the path of their research in order to win Framework funding. The government's chief scientist, David King, agreed that it was important to ensure the programme did not change the direction of British research.
He said: "There is money in the Framework 6 Programme for research that is not defined but we need to look at whether this is a large enough slice."
But Ian Halliday, chief executive of the Particle Physics and Astronomy Research Council, warned that the funding amounted to only 5 or 6 per cent of Europe's spending on science and should not be stretched too thinly. He said it should be "spread across areas where it can have most effect".
The committee heard evidence from universities complaining about the Framework 6 programme's "difficult and off-putting" application process.
The Scottish Executive launched a £1 million assistance fund to help overcome such problems and encourage Framework 6 applications in February this year.
But Sir David told the committee he had no intention of matching this funding in England. "I'm not sure there is a good argument in terms of priorities for investing science funds in this," he said.
The Biotechnology and Biological Sciences Research Council, the Medical Research Council and the Particle Physics and Astronomy Research Council also said they did not think they should be providing any extra money to ease these difficulties.
The UK government has put pressure on the European Commission to speed up and streamline the applications process, the committee heard.