European aviation has repeatedly been thrown into chaos in recent weeks by drone sightings and air incursions, including at airports in Copenhagen and Munich.
Air traffic at Vilnius was restored at 12.50pm AEDT on Sunday after a decision was made late on Saturday to close the airspace "due to a possible series of balloons heading toward Vilnius Airport," the operator said in a statement on its Facebook page.
Lithuania's public broadcaster LRT cited the head of the country's National Crisis Management as saying that 13 balloons were heading towards Vilnius airport.
According to notices posted to the US Federal Aviation Administration's website, the flight restrictions were due to "hot air balloon flights."
The Vilnius airport said the closure affected a series of overnight flights, with most incoming flights redirected to neighbouring Latvia and Poland, while departures were cancelled. One flight due to arrive from Copenhagen returned to Denmark.
NATO-member Lithuania in August declared a 90km no-fly zone parallel to the border with Belarus in response to drones entering from there, saying this would allow its armed forces to react to violations.
Lithuania, a strong supporter of Ukraine, shares a 679km border with Belarus, a close ally of Russia. The capital Vilnius lies roughly 30 km from the border.
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