Juncker also insisted that the huge South Stream gas pipeline to Europe could still be built, despite Russian President Vladimir Putin unexpectedly pulling the plug on the multi-billion-dollar project.
"Yes, Russia is a strategic problem for the time being and I hope that tomorrow Russia will be a strategic partner," Juncker said after talks with Bulgaria's Prime Minister Boyko Borissov, whose country stands to be one of those worst affected by the pipeline cancellation.
Juncker was asked about comments by Donald Tusk, the former Polish premier who took over as head of the European Council of EU leaders on Monday, who was quoted by the Financial Times as saying Russia had become a strategic problem.
After the end of the Cold War and the collapse of the Soviet Union, Russia and the EU signed a strategic partnership agreement in 1994 but that has been thrown into doubt by Moscow's intervention in Ukraine.
The 28-nation EU and the United States have imposed a series of economic sanctions on Russia over the crisis.
Bulgaria halted work on South Stream earlier this year after the EU said Sofia had breached the bloc's competition rules by the way it awarded contracts for its leg of the pipeline.
Juncker rejected Russia's comments, with the EU set to have a further meeting on the issue on December 9.
"South Stream can be built. The conditions have been clear since a long time. There is nothing new. The ball is in the court of Russia," he said.
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