Linkevicius met with Russian Foreign Minister Sergei Lavrov Saturday at the Munich Security Conference and said afterward that Lithuania and Russia have agreed to focus on their areas of agreement before tackling lingering disputes over security and energy issues.
"We agreed that our bilateral agenda and our bilateral relations should be intensified and strengthened," Linkevicius told the Baltic News Service.
It was the first official meeting between Lavrov and Linkevicius, who was named foreign minister under Lithuania's the new center-left government led by Social Democrat Prime Minister Algirdas Butkevicius.
Lithuanian voters returned the Social Democrats to power in October following four years under the center-right leadership of former Prime Minister Andrius Kubilius -- whose relations with Russia were strained -- in part by promising to improve relations with its neighbors.
Linkevicius appeared to give that process a push with his meeting with Lavrov, while at the same time acknowledging that big differences, primarily over the militarization of the Russian enclave of Kaliningrad and disputes over natural gas, remain.
"This does not mean that we can forget the differences, which, unfortunately, remain between us and there are a number of issues where our opinions differ," he said. "But we should strengthen our future relationship and try to find a common denominator where we have a consensus and try to look for positive examples for our agenda."
Among the areas the two sides can build on, he said, is an agreement that allows transit for Russian nationals traveling to and from Kaliningrad through Lithuania. The set-up has allowed them to make the trips without visas.
"This year marks the 10th anniversary of the simplified procedures for passenger transit to Kaliningrad and back," Linkevicius said. "This is a specific situation, at least in terms of Lithuania, that has been successfully operating for a decade."
Another is an effort to get rid of huge quantities of Cold War-era excess munitions remaining in Kaliningrad, where some 100,000 tons of unexploded ordnance have been designated for disposal.
But the Russian enclave is also a source of tension for Vilnius.
In December Lithuanian Foreign Vice Minister Vytautas Leskevicius voiced fears over the Kremlin's threats to install an S-400 surface-to-air missile system there should Russia be unable to reach an agreement with NATO on a joint European missile-defense shield, BNS reported.
"We stated our fears and our failure to understand Moscow's maneuvers to increase its attack munitions in Kaliningrad," Leskevicius told the news service after a meeting of NATO and Russian ministers in Brussels. "We see no strategic or defense sense in this."
Lithuania's new government also inherits a continuing legal dispute with Russia's state-owned Gazprom, which is fighting efforts begun under Kubilius to comply with the European Union's Third Energy Package deregulation push by separating the supply and transit functions of gas utility Lietuvos Dujos.
The company is majority-owned by Gazprom and German energy company E.ON.
The Lithuanian diplomat said his country's goal remains the energy market competition demanded by the European Union but added it will have to be accomplished with the cooperation of Russia, rather than unilaterally imposed by Brussels and Vilnius, BNS reported.