Top British universities say they have already faced problems working with European partners following the Brexit referendum result.
Academics said they had been asked to leave EU-funded projects or pull out of leadership roles.
In a confidential survey by the Guardian of Russell Group universities, reports of the backlash came from across the natural sciences, the engineering disciplines and social sciences.
The Russell Group is made up of the UK's 24 leading universities which have a commitment to high-class research.
Before the referendum, leading scientists and academics had warned that leaving the EU would cause a major funding blow to British universities and scientific research.
Anecdotes reported as part of the survey include an EU project officer recommending that all UK partners be dropped from research group because their share of the funding was not guaranteed, according to the Guardian.
In another case, a university reported that two social science collaborations with Dutch universities had been told partners from the UK were not welcome.
One university said that there had been "a substantial increase in definitive evidence" that EU projects were reluctant to collaborate with British partners.
Not all universities in the group responded to the survey and not all of those that submitted responses reported discrimination.