The US President telephoned the Prime Minister during the summer to try to persuade him that genetically modified (GM) crops - worth millions of pounds to the US economy - would not be bad for Britain.
The two leaders also discussed the matter during Mr Clinton's visit to Number 10 in May, Foreign Office officials have confirmed.
Sources close to the Government say that the US President is pressing Blair to support commercial production of GM crops in Britain despite growing consumer opposition.
Consumer and environmental groups including English Nature, the Government's official wildlife adviser, want the Government to introduce a moratorium on growing such crops commercially in the UK for at least three years.
France and Austria have temporarily banned the growth of GM food until more is known about its effects on the environment.
Clinton's intervention has outraged MPs and environmentalists. They accuse the US President of intruding in a sensitive domestic matter.
"It is quite wrong for the British Prime Minister to be conspiring behind the back of the British public about American business interests," said Norman Baker, Liberal Democrat environment spokesman.
The Clinton administration has close links with Monsanto, the powerful biotechnology conglomerate which develops the seeds for GM crops.
Monsanto, which made a profit of almost $300m (pounds 177m) in 1997, is one of five companies spearheading Clinton's welfare to work programme, and the President singled out the biotech company for praise during his State of the Nation address last year.
During the 1996 election, Monsanto was among those donating thousands of dollars in "soft money" (legal funds which are not included in the ban on corporate donations) to the Clinton camp.
MPs say Clinton's move is resonant of Tony Blair's telephone intervention earlier this year on behalf of media baron Rupert Murdoch. The Prime Minister sparked political outrage when he spoke to Italian premier Romano Prodi about Murdoch's bid to buy Mediaset, an Italian television company.
The first commercial GM crop, oil seed rape, is set to be sown in Britain next year, following Government approval. Hundreds of acres of trial crops have already been planted throughout the UK.Reuse content