Russian President Vladimir Putin said that the EU has to take "reciprocal steps" if it wants more access to Russia's energy market.
European Commission President Jose Manuel Barroso said there were still "sensitivities" that needed to be addressed.
The energy disputes have hung over the relationship since January, when a brief disruption in Russian gas supplies to Western Europe amid a price dispute with Ukraine.
Europeans fear excessive energy reliance on Russia, which supplies a quarter of Europe's gas. Meanwhile, Russia seeks access to the European retail gas markets.
Russia and the EU also signed key accords on easing visa rules and deporting illegal immigrants. The documents are expected to be ratified and come into force within a year.
(AP,AFP)