By Paul Rincon
BBC News science reporter
Lord Winston says science risks being tainted by commercial interests, in the same week the government claimed it was essential to the UK's economic success.
Lord Winston says basic research must not lose out
Launching National Science Week at London's Dana Centre, the fertility expert said these concerns were not being addressed properly by ministers.
The government has pledged £10bn to science over the next three years.
But critics have complained that most of the money will go to research in money-spinning areas like biotech.
"Too much commercial activity can actually diminish the value of research that is driven purely by universities. I think that is a danger," Lord Winston told journalists at a news conference.
"I'm not sure it's quite well articulated by the government at the present time. And I think that it is something they need to consider carefully."
Trade and industry secretary Patricia Hewitt announced how the overall £10bn science cake would be carved up between the different UK research councils on Monday.
But Professor Robin Lovell-Badge, head of genetics at the National Institute for Medical Research in London, and others said that little of the increased money would be available to fund basic research in science.
"To my mind, once one sees that science will drive our economy, it worries me too that that is seen as a major part of the whole science agenda," Lord Winston said.
"If we end up with too much commerce driving science, we may be driving it down avenues that are not always acceptable to everyone in our society."
Lord Winston said that GM crops were a prime example of an issue that many people had rejected because they connected the technology with commercial interests.
"People are generally very concerned about being driven for commercial reasons down a particular avenue where they can see risks but not many benefits," he explained.
The professor of fertility studies, who is based at Hammersmith Hospital in London, went on to say that universities were increasingly being encouraged to think about the commercial value in research.
"That results in research groups doing work that is valuable but not necessarily the best research that they can do. Rather it is research that attracts venture capital," he said.
"I don't actually believe that commercialisation is going to be a pivotal [funding source] on a large scale for a large number of universities.
"But it has the strings attached which often blur what scientists are trying to do."
Lord Winston was speaking as president of the British Association for the Advancement of Science (BA).
As part of National Science Week, over a thousand events are being held throughout the UK, including lectures, debates and demonstrations.