The House of Representatives has rejected government plans to cut investment in science and research over the next four years.
Academics and business leaders argue that trimming millions from the budget could jeopardise Switzerland's position as a centre for research.
The debate came as the government looks for ways to cut spending by SFr3.4 billion ($2.53 billion) over the next few years.
The government originally proposed investing SFr17.3 billion in education, research and technology during the four-year period between 2004 and 2007 - an annual growth rate of six per cent.
Now it's proposing cutting that sum by SFr480 million, which would basically mean a rise of only four per cent a year.
The House voted narrowly against the cuts. The issue will now go to the Senate.
"Everybody in the academic community was a bit surprised [by the proposed cuts]," Xavier Comtesse, director of the French-speaking section of independent think tank Avenir Suisse, told swissinfo.
"For a year, the politicians have told everyone that science and education is one of the first priorities and suddenly the money is going down again.
"During the past ten years, the state hasn't given enough money for science and higher education in Switzerland so basically it was very important that we had a huge increase."
"Education, research and technology are the very basis of Swiss prosperity," added Paul Herrling, head of research at pharmaceutical company, Novartis.
"While all our competitors are investing hugely, Switzerland has neglected these areas in the past few years and risks losing its position as a country that attracts the best brains."
Even a six per cent growth rate is well below what researchers say is necessary if basic research in Switzerland is to remain among the best in the world.
Annalise Eggimann, deputy director of the Swiss National Science Foundation, told swissinfo that Switzerland had lost ground to the United States and the Scandinavian countries over the past few years.
"We have to give young people a signal for the future," added parliamentarian Johannes Randegger of the centre-right Radical Party and a Novartis manager.
"The federal authorities must take their role seriously as far as education and training is concerned."
Politicians and scientists alike say that if Switzerland loses its research base, the country will have to import highly skilled people or risk seeing companies relocate abroad.
Last year, for example, Novartis decided to shift its research operations from Basel to the US state of Massachusetts.
"Switzerland is basically a country without raw materials so we need to have a highly skilled workforce," said Comtesse. "It costs a lot of money to educate people and basically there is no choice."
swissinfo, Vincent Landon
Academic and business leaders are concerned at government plans to slash the budget for education, research and technology.
They argue Switzerland's reputation as a centre of research is at stake, if funding rises only by an annual four per cent.
Scientists believe a lack of government investment has left Swiss science lagging behind on the international circuit.
The cuts are part of a government strategy to slash SFr3.4 billion ($2.53 billion) in spending across all departments.