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Boris Johnson wants a close research relationship with Europe, but the Northern Ireland dispute may cause the UK to walk away.
The UK should not abandon talks to participate in the European research programme, according to scientific leaders.
They told the British Broadcasting Corporation that being cut out of EU research would hurt British science.
The agreement in principle was reached, but the UK's involvement is now a bargaining chip in the talks.
The UK is ready to set up its own scheme according to the Science Minister.
Sir Jeremy Farrar, director of the Wellcome Trust, told the news organization that losing the agreement on UK participation in the world's biggest international science funding programme would be a huge blow.
He said that the government should plan for the worst-case scenario, but that any UK-only scheme would disadvantage our scientists compared to the international opportunities that the EU and many other countries take part in.
The EU's programme brings together researchers from industry and academia. The projects range from fundamental research to tackling societal issues.
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UK researchers will not be included in EU research projects because of the delay in joining the EU programme.
The UK's continued participation in the EU's programme was agreed in principle just before Christmas 2020. The signing off of a formal agreement on the UK's associate membership has taken a year.
Funding can't be released to the UK until there is a formal agreement. EU researchers will not include UK scientists in their projects if it becomes apparent that agreement will take many more months.
Cancer Research UK's chief executive said that exclusion from the European Union would be a blow to the fight against cancer.
It will put at risk the UK's position of being at the forefront of the global effort to improve the prevention, treatment and diagnosis of cancer.
The UK's position to collaborate and use science to address the global challenges will be weakened if the government does not strike a deal for continued membership of Horizon Europe.
According to some estimates, the UK has missed out on over one billion dollars of research funding since 2016 because of uncertainty caused by the UK's exit from the EU. Sir Jeremy said that ministers should not walk away from the talks.
The UK needs to stay in the game and resist the urge to shut the door on the game. It's the best way to support science and R&D in the UK.
Sir Jeremy responded to an article written by the science minister. If the EU stands in our way, the UK is ready to implement an alternative that is just as good or better.
The alternative was drawn up by Prof Sir Adrian Smith in case the EU refused to allow the UK entry into Europe. Prof Smith was elected President of the Royal Society, which represents the country's leading scientists. He said that most scientists would rather join the EU than the UK scheme.
Four decades of planning collaborative research with colleagues across Europe is what we have had.
The majority of UK researchers would find it hard to start a new programme from scratch because they would be competing with the prestigious schemes in the Europe programme.
It would take too long for Britain to set up its own scheme according to Dr Daniel Rathbone.
He said that the UK will lose top researchers and research groups as they move abroad to seek funding and collaboration opportunities elsewhere.
The chancellor's Autumn budget allocation of 2 billion dollars for the UK's membership of the European Union made it possible for a UK scheme to be started, but officials made it clear that the scientific community could spend the money they received. The decision to spend money on the European project was left to the scientific community by the Treasury.
Prof Smith said that if the uncertainty drags on into the new year, scientific leaders may have to consider a UK scheme.
He said that if the deal is not signed for another month or so, there will have to be a discussion.
Some may begin to think of an alternative as the uncertainty grows.
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