The head of a major research institute who categorically refused to allow any of his staff to apply for European Commission research funding. The science grandee who stood down from an advisory council in disgust at the paperwork. The highly regarded bright young scientist who was successfully awarded a grant but never took it up because others spotted his potential before the Euro-paperwork could be completed.

These are just a few examples of accumulated bad will and lost opportunities from decades of the Brussels experience. The principle of pan-European research collaboration, policy and infrastructures is laudable. The practice is dreadful.

In the wake of a 1999 corruption scandal involving the then research commissioner Edith Cresson, the European Court of Auditors demanded an increase in the already strict level of financial control across European Union (EU) programmes. New EU financial guidelines were introduced in 2004, requiring the sort of detailed accounting that leaves no room for corruption. As a consequence, every cent in a research project has to be justified and accounted for both before and after it has been spent.

Current examples of that burden are all too easy to find. Following the discovery of a small number of accounting errors, the European Commission has instigated a mammoth re-audit of hundreds of completed projects — for example, the CNRS, the French research agency, is now having to audit about 900. This effort is out of all proportion to the amounts of money in question. Or consider the large projects in the current Framework research-funding programme. These require immense amounts of pre-auditing, leading to applications more than 100 pages long.

But it is when the applications succeed that the bureaucratic floodgates really open. The documentation provided in the approved project application must be updated at the end of each year, with explanations of why estimates of individual person-months may have slipped, why plans for costed new instruments might need to be changed and why exactly various deliverables have been delayed, or modified or transferred between partners. The following year's money will not be released until this documentation is submitted and approved — a process that can take weeks.

The fear of criticism from the Court of Auditors is a miasma that envelops the commission, and in turn greatly undermines the motivation of the researchers it seeks to engage. Many scientific officers in Brussels are sympathetic and have managed to introduce some slight improvements, but their hands are tied. Moreover, others adopt a much more precautionary and burdensome interpretation.

The plain fact is that this rules- and process-based approach, appropriate enough for projects whose outcomes can be specified, is misguided in respect of research, whose outcomes are uncertain by definition. Risks that an investment might return less than hoped come with this territory, and need to be embraced as part of a funding culture by those ultimately responsible for the Brussels machine: its political overseers in the European Parliament and the council of ministers.

Here is an opportunity for the new research commissioner, Máire Geoghegan-Quinn, to take the initiative. The commission has already made high-level overtures to the European Parliament that point in the right direction. The Court of Auditors is sympathetic to 'simplification', and so too are elements in the European Parliament, where the committees responsible for budget and for research are influential.

The council of ministers will be another key element in building the political momentum for change. These EU member-state ministers need to fully appreciate that the burdens of bureaucracy are sufficient to constitute a real threat to the future of the commission's programmes. The new research commissioner is (by her own account) an energetic politician who also brings experience as a member of the Council of Auditors. She is on a steep learning curve. But if she can catalyse the political change in attitudes required, and embody them in risk-tolerant financial guidelines, she will have achieved something more visible and significant than most of her predecessors. Any country whose researchers and administrations see value in these research programmes should support her.