In particular, the summit was overshadowed by Moscow's disputes with three recent EU members - Poland over a Russian ban on its meat, Estonia over the removal of a Soviet war memorial from the center of its capital Tallinn, and Lithuania over its demand that Russian oil deliveries be resumed via the Druzhba pipeline.
At the start of talks at a health spa near the Volga city of Samara, Putin pledged to hold "an open and sincere dialogue without any taboo subjects" with EU leaders, including Chancellor Angela Merkel of Germany, which holds the EU rotating presidency, and the president of the European Commission, Jose Manuel Barroso.
After the talks, no joint declaration was drawn up, in contrast with usual practice. However, the Russian president denied that the summit had failed to produce any results.
The sides had previously hoped to launch talks on a new EU-Russia partnership agreement, but a veto on the talks from Poland over Russia's embargo on its meat exports remains in force, and the EU leadership reiterated its support for Poland and other members involved in current rows with Russia.
"It is very important if you want to have close cooperation to understand that the EU is based on principles of solidarity," Jose Manuel Barroso said.
Commenting on prospects for a new Partnership and Cooperation Agreement (PCA), German Chancellor Angela Markel said the EU was interested in starting talks on a new cooperation agreement despite a number of issues still hampering negotiations.
"We want negotiations on a new Partnership and Cooperation Agreement to be resumed... and we have no doubts that this must happen," Merkel said.
Leaders of the EU, increasingly concerned over energy security, are also pushing for Russia to sign the Energy Charter, which would compel the country to open up its vast oil and gas reserves and pipeline network to European companies and to provide safeguards for investors.
EU officials have reportedly warned they will add the main clauses of the Energy Charter in the agreement's new draft if Russia does not sign the energy treaty. Moscow has so far resisted, saying the agreement runs counter to its interests.
The European Union, which imports more than a quarter of its oil and natural gas from Russia via Ukrainian pipelines, faced a brief disruption last winter when Moscow suspended gas deliveries to Ukraine over a price dispute, sparking doubts over Russia's reliability as a supplier.
However, Russia, which has restricted European companies' access to its energy sector, insists that energy security works both ways, and wants Europe to offer purchase safeguards for its energy if it wants Russian producers to guarantee steady deliveries.
President Putin reiterated that Russia would protect its interests in the same way that the EU does, considering the number of complex issues within the EU.
"The European Union has changed, the number of members has increased, and it is more difficult to resolve the issues that were easy to settle in the past," Putin said. "However, we must defend our own interests as professionally as my [European] colleagues do."
The Russian leader criticized the EU for not fulfilling its obligations under the Energy Charter, citing Europe's failure to open the nuclear materials market by 1997 and give Russia direct access to it.
POLISH MEAT BAN
Putin also said the row between Russia and Poland over Moscow's ban on its former Eastern Bloc ally's meat exports was a common economic issue rather than a political matter. Last November, Warsaw vetoed new PCA talks over Russia's ban on meat and other agricultural imports from Poland. Moscow cited health concerns, but Warsaw said the move was political.
"We all know that there are many disputes within the EU and between the EU and other countries on agricultural issues," Putin said, adding that a common approach to resolving these issues should be developed and used by all concerned parties.
But Jose Manuel Barroso said Russia's embargo on Polish meat imports was unjustified.
"If there were grounds [for an embargo], we would not allow Poland to circulate meat in the European Union," he said after the Friday summit.
Putin said Russia was ready to continue talks on its embargo on Polish meat imports, but expected closer cooperation and understanding from Poland and the EU.
"We have not yet solved the Polish meat problem, since our Polish colleagues have not been on speaking terms with us for over a year" Vladimir Putin said. "Thank God, there is the German Chancellor representing their interests. We will move further."
Russia remains one of the key economic partners of the European Union after the U.S. and China, and has been successfully cooperating with Europe on a variety of political, economic, cultural and humanitarian issues.
The EU reaffirmed its concerns over the alleged rollback of democracy in Russia, citing the widely publicized murders of journalist Politkovskaya, ex-FSB officer Litvinenko and the brutal handling of anti-government protesters by the Russian police.
Europe and the United States have consistently reproached President Putin for his clampdown on democratic freedoms. European officials have also attacked the Kremlin for increasing control over the press and suppressing the opposition.
But Putin brushed off the criticism Friday, saying that he had nothing against opposition actions as long as the protesters abide by the law.
"I think such actions [as opposition protests] must be organized within the law, and should not interfere with other people's everyday lives," the Russian leader said.
Meanwhile, Western media reported that Russian police prevented Garry Kasparov, the leader of the United Civil Front opposition movement and a former world chess champion, from boarding a plane in Moscow to Samara.
An official spokesman for the police department overseeing Sheremetyevo airport confirmed the detention. "We had suspicions that the tickets were fake," he said, adding that opposition leaders had been released and could have boarded later flights if they wanted to.
Putin tried to justify police actions by saying: "Police and law enforcement agencies in Europe also take preventive measures."
Putin, who has led Russia for seven years and enjoys the support of a majority of Russians for the stability and economic growth Russia has had during his tenure, said people in power were responsible for how they handle protests and promised that those who want to organize protests in Russia would have the opportunity to do so.
Putin reiterated Russia's position that violating the rights of Russian communities in Latvia and Estonia was inadmissible and unworthy of Europe.
"We reiterated our position at today's meeting. We consider [Baltic discrimination against Russian communities'] inadmissible and unworthy of Europe," Putin said.
The Russian leader brought up another sensitive issue - the death of an ethnic Russian in Estonia, now a EU member, during protests against the removal of a Soviet monument in April. Putin said it was "murder." Estonian police denied any involvement.
Russian authorities have expressed serious concerns about Estonia sanctioning SS marches, which Moscow sees as support for Nazism. Tallinn responded by saying that it sees no difference between Soviet and Nazi occupation.
However, Jose Manuel Barroso, the president of the European Commission who also attended the summit, stood up for Estonia, saying no EU country backed Nazism, but condemned any demonstrations in favor of Nazism or neo-Nazi regimes.
German Chancellor Angela Merkel said that hopefully Russia and certain EU countries would settle their disputes with a view to establishing a strategic partnership.
"We have a mutual understanding that we should establish a strategic partnership," Merkel said. She said she was glad an open and sincere dialogue was possible, even if differences remained.
President Putin denied speculations that the Russia-EU summit had produced no agreements. "We agreed on nearly all issues, except sensitive ones that require additional study," he said. "These are mostly problems that stem from economic selfishness."
He said Russia and the EU planned to establish a mechanism for exchanging information and early warning in energy, and that the two parties had agreed to exchange advance electronic information to speed up the cross-border transit of goods, and to speed up work on border cooperation programs.
He also said both sides were stepping up negotiations on a transition to a visa-free regime ahead of a relevant agreement, which comes into effect June 1.
Jose Manuel Barroso reaffirmed that the European Union fully supported Russia's accession to the World Trade Organization, pointing to certain progress in many spheres, including common economic and investment contacts.