"This issue demands a solution. The ball is in our court, and we may provide an answer before the summit in Portugal. The problem exists and we will work to solve it," he told a news briefing.
The EU-Russia summit will be held on October 26.
President Vladimir Putin ordered the imposition of export duties on raw timber in March, after saying he wanted to promote the development of the domestic wood-processing industry. The move angered EU members Finland and Sweden, whose pulp and paper industries process large amounts of Russian timber, and has become an obstacle to Russia's bid to join the World Trade Organisation.
Mr Medvedkov rejected accusations from Sweden that the duties violated earlier agreements between Russia and the EU.
"Russia had the full legal right to do this," he said. "All our agreements with the EU on the issue will only take effect when Russia joins the WTO.Russia, the world's ninth-largest economy, is the largest country outside the WTO. Moscow has been in membership talks since the mid-1990s and officials now hope to complete entry formalities next year.