At a ceremony, Defence Minister Juozas Olekas welcomed the ships -- four minesweepers and a support vessel from Norway, the Netherlands, Belgium and Estonia -- as NATO seeks to reassure Lithuania and other jittery member states in the region.
"The arrival of NATO ships is yet another sign of NATO unity and solidarity," Olekas told AFP by phone after the ceremony in the western port city.
He called NATOs increased presence a "deterrence measure" against Russia, which has an estimated 40,000 troops massed on Ukraines eastern border.
NATO deployed the naval group to the Baltic Sea last week, saying it indicated "the alliances commitment to the safety and security of the Baltic member states".
The Lithuanian defence ministry said the NATO ships would also visit other Baltic ports and participate in a mine-hunting operation in neighbouring Latvia later this month.
About 600 US troops have been sent to Lithuania, Latvia, Estonia and Poland in recent weeks, while Britain, France and Denmark have sent extra fighter jets.
British defence minister Philip Hammond will visit his troops at Lithuanias Siauliai air base later on Friday.
Russian actions in Ukraine have rattled nerves in the Baltic states, which were occupied and annexed by Moscow during World War II.
The three countries -- Lithuania, Latvia and Estonia -- broke free from the crumbling Soviet Union in 1991 and joined both the European Union and NATO in 2004.