The Royal Society president has called for the UK government to underwrite the research of all UK-based researchers who apply for EU funding now.
Speaking in an interview with BBC Newsnight, Prof Sir Venki Ramakrishnan, said post-Brexit uncertainty needs to be "nipped in the bud".
He said EU researchers based in the UK also need to be given assurances that they will be able to stay indefinitely.
The Royal Society is a key advocate for science in the UK and the world.
"We're hearing about UK researchers being excluded from collaborations because their other EU collaborators don't want to take on a UK-based researcher because they don't know what their status will be," said Prof Ramakrishnan.
"Of course, this isn't strictly speaking legal because we are still part of the EU. But you can't police this. If somebody doesn't want to take on a British researcher because they think it's too risky, they simply won't."
Prof Ramakrishnan - who shared the 2009 chemistry Nobel Prize for his work on ribosomes - said: "The UK could simply say if there are UK-based researchers who apply for EU funding now, then we will underwrite that funding until the end of the grant, regardless of what happens with negotiations.
"That wouldn't cost a lot of money, but it would certainly resolve this uncertainty about their status."
Prof Ramakrishnan has been president of the Royal Society since December 2015. The position is one of the most important in British science.
He said there is also "anxiety" among EU researchers based in UK who feel "dispossessed" and "vulnerable" following the referendum result - meaning that the best talent is "poachable" by other countries.
"I think it's very important for the UK government to send them a strong signal that they are going to be welcome here indefinitely, over the long term," he told Newsnight.
"We don't want this situation to snowball as a result of uncertainty.
"I cannot emphasise this strongly enough, because we are in a global market for talent, and if we are perceived as a xenophobic country, then we will be less attractive - not just for science and researchers - but also for investment, for business, for all sorts of things."
Last week, the UK's national academies representing science, medicine and engineering sent a joint letter to the government saying that Brexit is harming science.
Watch more of BBC Newsnight's interview with Prof Sir Venki Ramakrishnan on the programme tonight at 22:30 BST on BBC Two - or catch up afterwards on iPlayer.