Putin told a news conference he "deplored" the lack of progress but said Russia will be patient.
Poland blocked an EU negotiating mandate for the partnership agreement because Russia refused to lift its embargo on meat imports from the country.
European Commission President Jose Manuel Barroso told reporters he had appealed to Putin to lift the ban on Polish foods imports.
Finnish Prime Minister Matti Vanhanen, whose country holds the rotating EU presidency, said the two sides held "fruitful and frank" discussions on a wide range of issues, including energy, where he said "there is a common understanding that our energy partnership is based on strong and positive interdependence."
Vanhanen said EU leaders discussed human rights, democracy, and the rule of law with Putin.
He said concerns also were raised about Russia's probe into the murder of investigative journalist Anna Politkovskaya.
(compiled from agency reports)