Putin said: "We say to all: partnership, cooperation and teamwork - yes."
On the day Serbia voted in parliamentary elections, Merkel said she hoped the vote would boost democratic forces in the Balkan country.
"There were irritations at the start of the year, and I made it clear from my side... communication in such situations must be improved to avoid such irritations"
Angela Merkel, German chancellor, speaking on Russia's closure of an oil pipeline
Putin said any solution on the status of Kosovo would have to be acceptable to Serbia – a stance which could block an anticipated UN proposal to give Kosovo a measure of independence opposed by Belgrade. Russia holds a veto in the UN Security Council.
Merkel, holder of the EU's rotating presidency, referred to Moscow's decision earlier this month to shut the Druzhba oil pipeline to northeast Europe during a dispute with transit country Belarus.
"There were irritations at the start of the year, and I made it clear from my side. I believe we agree here that communication in such situations must be improved to avoid such irritations," she said.
Putin allayed some of the EU's concerns by saying Russia would accelerate work on new export routes to the West.
He said Moscow was committed to building its energy relations on the basis of clear rules.
"We always say... we want to operate on the basis of a clear, market relationship... clear principles applicable to all," he said.
Putin did address details about what rules Russia was prepared to sign up to, a key issue for energy customers.
Relations between the EU and Russia have been complicated by Poland vetoing the start of talks on a new long-term partnership agreement between Russia and the bloc.
Poland blocked the talks in protest at a ban Russia imposed on Polish meat imports.
Russia cites food safety concerns as being behind the decision.