The European Commission has put its two decision-making bodies on a crash course by refusing to restart controversial patent legislation, despite a formal European Parliament request for it to do so.

Soon after, the other side, the Council of Ministers, made it clear it would not back down without a fight and announced it was planning to push ahead with its version of the directive by formally adopting an agreement reached in May last year.

Campaigners against the directive had managed to persuade MEPs to vote to restart the decision-making process from scratch to prevent patent protection being extended to software. There weren't happy with the news. Florian Müller of NoSoftwarePatents.com said that the Commission had decided to "negate democracy" by ignoring MEPs' request.

European Commission president Jose Manuel Barroso sent a letter to the President of the European Parliament, Josep Borrell, on Monday, saying that the Commission "did not intend to refer a new proposal to the Parliament and the Council [of Ministers]" as it had supported the agreement reached by ministers in May 2004.

The letter added that the Commission expected the Council to formalise the May agreement as soon as possible so that the next stage of the decision-making procedure could continue.

However, the Commission's decision is risky because Barroso already faces opposition to his pro-free market policies from the Parliament's second biggest group, the Socialists, plus the Greens and the Communist-dominated European United Left-Nordic Green Alliance.

The decision to ask Barroso to submit a new proposal was backed unanimously by all political groups in the Parliament following an overwhelming vote in favor of the request in the Parliament's legal affairs committee. The Socialists may decide to escalate the dispute into a wider political fight.

Maria Berger, an Austrian Socialist MEP, and member of the legal affairs committee, said that the Commission's decision would not lead to a "good solution". French Green MEP Alain Lipietz warned two weeks ago that if the Commission ignored the Parliament's request it would be an "insult" to the assembly. He said that the Parliament would then reject the Council's version of the legislation as part of the final or conciliation stage of the co-decision procedure.

The Commission's decision to ignore the Parliament also throws the whole issue into legal uncertainty because it is not clear whether MEPs can block the decision-making procedure by refusing to recognise the Council's agreement.

Luxembourg, which is currently chairing European Union meetings, has said it wants to try to get the May deal formally adopted at the 7 March meeting of the Competitiveness Council. This would normally mean that the second reading stage of the process could start, giving MEPs and the Council another chance to come to an agreement about the scope of the directive.

However, this could be blocked if the Parliament president refuses to recognise the Council's position.