Incursions by balloons carrying contraband cigarettes prompted the Nato and EU member state to close Vilnius airport four times last week and temporarily shut its border crossings with Belarus.
"Today we have decided to take the strictest measures, there is no other way," Inga Ruginienė said on Monday, adding that her government may also discuss invoking article 4 of Nato's treaty to call security consultations.
Vilnius has said the balloons are being sent by smugglers, but blames the authoritarian president of Belarus, Alexander Lukashenko, a close ally of the Russian leader Vladimir Putin, for not stopping them.
Ruginienė told a press conference the incidents were "hybrid attacks" and announced the closure of Lithuania's Belarus border crossings except for travel by diplomats and by EU citizens leaving the neighbouring country.
Flights in and out of Lithuania's main airport were disrupted on Friday and again on Saturday night in the latest of a string of incidents involving suspected sightings of cigarette smugglers' balloons, leading to dozens of cancellations and diversions.
Those incidents followed similar disruption early last Wednesday morning and on other recent occasions, leading to the closure of Lithuania's two border crossings with Belarus, at Medininkai and Šalčininkai, for several hours.
Lithuania, which borders Russia's Kaliningrad exclave as well as Belarus, also summoned a Russian diplomat last week in protest at what it said was the entry of two Russian planes into its airspace on Thursday.
The country's defence ministry said a Sukhoi SU-30 fighter and an IL-78 tanker from Kaliningrad passed through Lithuanian airspace for 700 metres (2,300 feet) before leaving after 18 seconds, probably during aerial refuelling training.
The foreign ministry said it had summoned Russia's chargé d'affaires and issued a "strong protest", urging Moscow to explain the reasons for the violation immediately and take "all necessary measures to prevent such incidents from happening again".
Russia's defence ministry denied the incursion had taken place. "The flights were conducted in strict compliance with the rules for using airspace above Russian territory. The aircraft ... did not violate the borders of other states," it said.
The three Baltic countries, which are Nato members and firm supporters of Ukraine, have all been exposed to violations of their territory by Russian planes or drones. Three Russian MiG-31 fighter jets spent 12 minutes in Estonian airspace in September.
European aviation has repeatedly been thrown into chaos in recent weeks by drone sightings and other air incursions, including at airports in Copenhagen, Munich and the Baltic region. Moscow has previously denied involvement.
Lithuania's foreign minister, Kęstutis Budrys, said on Monday that recent airspace violations should not be regarded as isolated incidents. "These are calculated provocations designed to destabilise, distract [and] test Nato's resolve," he said.