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Speaking at the European Patent Forum in Munich, she called for rapid reforms to the European Patent system, while stressing that the quality of the patents must not suffer.
She said, "the European patent system must be improved" as part of a comprehensive European innovation strategy and urged other European countries to work together to make the Community patent a reality.
"We are so proud of the diversity in Europe, but the Community patent is one point where this diversity could be reduced a little," she said, adding that the key challenge is making the system "standardised, more affordable and legally secure".
Ms Merkel noted that the framework for the reforms had already been defined in the European Commission's hearing last year. She said that with more than 2 500 contributions submitted by companies and organisations, "there certainly wasn't a lack of interest".
Noting that translations costs currently account for up to 40 per cent of the cost of a patent, Ms Merkel said that she and Justice Minister Brigitte Zypries would fight to see the London Agreement realised.
"We won't settle for a half-hearted compromise," she said, calling the London Agreement "an important step in the right direction".
The German chancellor also expressed her support for the European Patent Litigation Agreement (EPLA), saying: "Where there is a will, there is a way."
"All parties must be able to rely on the fact that disputes can be brought before a common European court of law."
Ms Merkel, who has made innovation one of the key themes of the German EU presidency, told the conference that the quality of European patents must not decline. "I welcome the European Patent Office's approach of upholding the quality of its patents despite the growing number of applications," she said.
Around 400 participants attended the European Patent Forum at the EPO's headquarters on 18 and 19 April to discuss the future of the patent system and IP in general.