Scientists in the Czech Republic are up in arms over drastic changes in the national science-funding system that they say will damage basic research in the long term.

Jiří Drahoš fears that budgets will be cut still further.

Starting next year, core funding for Czech universities and research institutes will be allocated according to rigorous metrics. Institutes can obtain 'points' for a variety of publications and for patents, but also for any software, methods, samples, prototype devices and 'validated technologies' developed in-house. The government plan, drawn up over the past three years with the goal of increasing the efficiency of research and development, was approved by the Czech cabinet on 29 June.

But critics say that the prescribed funding formula gives a grossly distorted picture of the real assets of Czech science, and threatens to destroy its best parts. Ill-defined criteria of 'innovation' will downgrade the merit of detailed work on books and peer-reviewed papers, they argue, while rewarding impressive-sounding concepts and rushed patent applications.

"One general formula for all branches of science?" says Jan Konvalinka, a group leader at the Academy of Sciences of the Czech Republic's Institute of Organic Chemistry and Biochemistry in Prague. "That's almost alchemy."

The academy, which runs 54 basic-research institutes, will be hit badly. In 2010, it will lose 1 billion Czech koruny (US$54 million), or about 20% of its annual budget, as a result of the new scheme. Academy president Jiří Drahoš says that in future years the number could climb to 45% of the value of the current budget.

"If this new formula is strictly applied, we will enter into a liquidation spiral," he says. "At some point the academy just cannot work anymore."

At a crisis meeting last week, the academy's leadership decided to stop paying for repairs and procurement, including purchasing scientific equipment, starting in January. If budgets continue to decline, staff may have to be laid off, says Drahoš.

The reform comes from a council chaired by Jan Fischer, the Czech prime minister, and comprising representatives from universities, the academy and industry. Initially, applied and industry-oriented research were supposed to be strengthened without affecting basic research. Changes included reallocating science portfolios to the industry ministry and creating a new technology agency.

The government had said previously that public-science budgets would increase by 2 billion koruny per year, to 31 billion in 2012. But the economic crisis has thwarted the plan, and science expenditure is now frozen at 25 billion koruny per year.

The freeze follows several prosperous years for Czech science, which has experienced a notable upswing since the country entered the European Union (EU) in 2004: it now spends around 1.4% of its gross domestic product, up from 1.2% in 2003, on research and development. This is more than any other formerly socialist, eastern European country in the EU.

Critics say that the new system is a step backwards. "It started out as a good idea, but then it got screwed up in the hands of technocrats," says Pavel Jungwirth, a computational chemist at the Institute of Organic Chemistry and Biochemistry.

Jan Zrzavý, a biologist at the University of South Bohemia in České Budějovice, who was on the government council that drafted the reform, declined to comment, saying that transferring the discussion to an international forum would be "ill-calculated and potentially harmful".