Government funding for Swiss scientists engaged in cross-border European Union projects has fallen short for the first time since European research framework programmes began in 1992.
The federal administration in Bern said the shortfall was being addressed, but researchers fear Switzerland could be seen as an "unreliable partner" by Brussels in future.
Paul-Erich Zinsli, vice-director of the federal ministry for education and research, said the underfunding was a result of changing from one regime to another.
Dr Zinsli said that since Switzerland became an associate member for EU research programmes in January 2004, funding commitments for its researchers already involved in lengthy projects with other European countries, had increased.
Until January, all Swiss researchers whose project proposals were approved in Brussels were underwritten entirely by the Swiss government, as their third-country status did not entitle them to money from EU sources.
Bern has set aside CHF100 million (£43 million) a year for Switzerland's Brussels-approved researchers, and their number has steadily increased.
But from the beginning of January, all applicants approved by Brussels will receive 100 per cent EU funding. Switzerland now has to pay an annual contribution based on a percentage of gross domestic product to the EU - reckoned at CHF200 million-CHF220 million - and will cease to make national financial commitments to Swiss-EU projects.
Many Swiss researchers are concerned that even though their projects have been approved by the EU, they will not receive the additional funds already promised by Bern in 2003.
"I can't sign any contracts or hire any PhDs until I know what is happening," said Domenico Giardini of the institute for geophysics at the Swiss Federal Institute of Technology Zurich.
Professor Giardini, an experienced adviser on natural catastrophes prevention to the EU, said: "The Swiss government can't tell its scientists to go and get EU grants and then not come through with the money. I'm optimistic they'll find a solution - it would be very unusual if the Swiss did not find a solution for this."
Sofia Karakostas, head of Euresearch, the Swiss national contact point for EU research at the institute, also said that administration was confident the funds would be paid retrospectively. "It is a very positive situation for Switzerland because the number of projects approved by Brussels is much higher than expected."
But Mr Zinsli conceded that, because of the large national deficit, there were funding cutbacks across the board in Bern . He said his ministry might have to renegotiate financial packages with individual research groups.
Ms Karakostas predicted that EU-approved research projects would have to turn to their home institutions to bridge the upcoming gap in funding if Bern withdrew from its 2003 commitments.