Ending a 30-year stalemate to get the new system approved, the ministers struck a deal after agreeing that they would set up a common European court for patent decisions by 2010.
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"We have a common approach," Hansjoerg Geiger, German secretary of state for the justice ministry, told reporters on the sidelines of a meeting of EU industry and research ministers.
The issue of the common court was the final one to be solved. Another sticking point had been over the language to be used in the patent.
The ministers struck a broad agreement, but technical details still have to have worked out before formal adoption of the law expected later this year.
The Commission says a system of EU patents will reduce the cost of getting patent rights for inventions in the bloc to 25,000 euros from 50,000 euros.