Still, a common patent system, despite some flaws, should hold huge advantages over the national system as it exists now. Patents protect the rights of inventors and are seen as a key to fuel creativity and innovation.
EU officials said that the current complicated EU patent approval now costs about €36,000 ($46,800) compared to some €1,800 ($2,300) in the United States and some €600 ($800) in China.
The U.N.'s World Intellectual Property Organization highlighted on Tuesday how the EU is lagging behind on patents.
China's patent office received 526,412 applications in 2011, ahead of the United States with 503,582 filings. In contrast, the European patent office had 142,793 applications in 2011, down 5.4 percent from 2010.
"One of the reasons for this difference is without a doubt the prohibitive cost and the complexity of obtaining patent protection," he said.
Under the new rules, patenting costs could come down by up to 80 percent once the system kicks in at the beginning of 2014, said Cecilia Wikstrom, of the ALDE liberal group in the European Parliament.
"A common European patent is key to strengthening Europe's competitiveness in a globalized world. We must be able to compete with the U.S, Japan and other developed countries,"Wikstrom said.