The most senior cardinal in the Vatican met NATO troops in Lithuania on Saturday, delivering a message of peace in the Baltic region amid tensions with Russia.

Secretary of State Cardinal Pietro Parolin met Portuguese troops at the northern Siauliai air base which hosts NATO's Baltic air police mission patrolling the alliance's frontier with Russia.

NATO jets at the base have been scrambled with increasing frequency to intercept Russian aircraft since tensions with the West soared after Moscow's 2014 annexation of the Crimean peninsula from Ukraine.

"This visit is meant to be a meeting with persons who work here, and at the same time a sign of peace," the cardinal told reporters, speaking in English.

"There are so many conflicts, so many clashes between peoples and persons that really we need mercy as an instrument of pacification and understanding," he added.

Mercy is the official Vatican theme of Holy Year, which runs until the end of November.

Lithuania and fellow Baltic EU states Latvia and Estonia have been alarmed by Russia's annexation of Crimea in 2014 and support for pro-Kremlin rebels in eastern Ukraine.

They have recently secured additional military resources from NATO, angering Moscow which accuses the US-led military alliance of trying to contain it ever since the collapse of the Soviet Union.

Baltic states, who were under Soviet occupation during the Cold War, lack sufficient aircraft and allies have been guarding their skies since 2004 when the trio joined the defence alliance.

Portugal and Britain took over responsibility for providing air policing from May, offering four fighter jets each in Lithuania and Estonia.

Lithuania's foreign minister Linas Linkevicius, a vocal critic of Russia, said the cardinal's visit showed Vatican was attentive to regional security.

"It can be seen as a certain political signal taking into account the importance of this mission to the security of the Baltic states," the minister told AFP on Saturday.

Parolin on Saturday also met Lithuania's Prime Minister Algirdas Butkevicius and visited the Hill of Crosses, a famous Christian pilgrimage site.

The cardinal, who is second only to Pope Francis, will celebrate mass at the central square in the capital Vilnius on Sunday and will meet the Baltic state's President Dalia Grybauskaite on Monday.

Lithuania, where 77 percent of the three-million-strong population is Roman Catholic, has invited Pope Francis to visit the country in 2018 when it celebrates the centenary of its first restored statehood.

The country has restored its independence from Moscow twice -- in 1918 and 1990.