Putin, playing the gracious host, opened today's meeting by welcoming the chance for open dialogue between Moscow and Brussels.
By the afternoon press conference, however, his tone had grown more critical.
"We discussed the extremely important subject of the violation of the rights of the Russian-speaking population in Latvia and Estonia," Putin said. "Our position is well known and we reiterated it at the meeting today. We consider it unacceptable and unworthy of Europe."
The Russian president's remark follows weeks of controversy over EU member Estonia's decision to relocate a Soviet-era monument from a central street in the capital Tallinn. The decision sparked mass rallies in Estonia, during which an ethnic Russian was killed. Putin today called on those responsible to be brought to justice.
Estonia is just one of the new EU member states to antagonize Russia ahead of the summit. Poland, for its part, has blocked talks on a Russian-EU strategic partnership agreement in response to a ban imposed by Moscow on Polish meat imports.
Dim Hopes From Start
Those disputes, as well as continued disagreements over the future status of Kosovo and energy security, lowered expectations for today's summit meeting between Putin, German Chancellor Angela Merkel, European Commission President Jose Manuel Barroso, and other EU officials.
Chancellor Merkel, representing the current EU presidency, said she hoped Russia would resolve its differences with individual EU states and move ahead with a strategic partnership with Brussels.
"I want to emphasize once more that, naturally, we are interested in negotiating a new partnership agreement," Merkel said. "We have discussed various issues here about several member states that fall under the [EU's] responsibility that have yet to be solved and on which we need to continue working."
The two sides did agree on concrete economic cooperation measures such as simplifying border controls and exploring ways to facilitate investments. More generally, they vowed to continue constructive dialogue despite continued differences.
Barroso praised the talks as "open" and "honest."
"It was important to have this summit. There were very open, very frank, very honest exchanges," he said. "We could see the progress that we have been achieving in many areas, namely, [that] the overall economic, trade, an investment relation is developing well."
Opposition Leaders Detained
Some observers focused not on the summit, but the sidelines, where some 200 opposition activists gathered for a March of Dissent rally.
The rally was officially sanctioned, but followed a week of crackdowns against activists in Samara and elsewhere.
Former chess champion Garry Kasparov, now a leading figure in the Other Russia opposition movement, was detained this morning at Moscow's Sheremetyevo Airport as he was attempting to board a plane to Samara.
Officials have claimed Kasparov's ticket was improperly issued. Several Western journalists and other opposition figures were also barred from boarding the plane.