Lithuania told residents in central and northern parts of the country to seek shelter for about an hour on Sunday morning after an unidentified flying object entered its airspace, the army and national crisis management center said.
The object was likely a drone which entered from Poland, defense minister Robertas Kaunas told reporters, adding that he had proposed a joint investigation with his Polish counterpart.
Poland's military said it was also verifying a possible violation of its airspace by an unidentified object.
During the "red" alert, NATO air police fighters were scrambled to the area and Kaunas airport, near Lithuania's second-largest city, was temporarily closed, the crisis management center said.
The NATO aircraft were unable to visually identify the object due to cloudy weather and did not attempt to shoot it down, the center said.