Lithuania’s president and prime minister were rushed to underground bunkers and residents of the capital, Vilnius, urged to take shelter during a warning issued after a drone violated the country’s airspace.

Air and train traffic in and around the city was suspended after the mobile phone “take shelter” alert, the first issued in an EU and Nato country since the start of Russia’s 2022 full-scale invasion of Ukraine.

“Air raid alert! Go immediately to a shelter or a safe place, take care of your family members and wait for further instructions,” read the defence ministry’s warning, which was sent at about 10.20am on Wednesday and lasted for about an hour.

Schools brought children to designated shelters, people in office and apartment buildings went down to basements, and Lithuania’s president, Gitanas Nausėda, and prime minister, Inga Ruginienė, were rushed to bunkers along with cabinet members and MPs.

The president of the European Commission, Ursula von der Leyen, said after the alert that Russia and Belarus had been directly responsible for a spate of drone incursions into EU and Nato countries’ airspace during recent weeks.

Russian electronic jamming has been blamed for the Ukrainian drones crossing into Finland, Estonia, Latvia and Lithuania, all of which border Russia. A Nato jet shot down a drone over Estonia on Tuesday, while Latvia’s prime minister resigned last week over the incursions.

“Russia’s public threats against our Baltic states are completely unacceptable,” von der Leyen said on social media. “Russia and Belarus bear direct responsibility for drones endangering the lives and security of people on our eastern flank.”

Nato’s secretary general, Mark Rutte, said on Wednesday that even if drones crash-landing in the Baltic states had been launched by Ukraine, they were “not there because Ukraine wants to send a drone to Latvia, Lithuania or Estonia. They are there because of the reckless, illegal, full-scale attack of Russia.”

Some EU and Nato members said a more forceful response might be necessary. Poland’s prime minister, Donald Tusk, said on Wednesday: “The Ukrainian-Russian war may soon lead to a situation where we will have to react firmly.”

Lithuania’s army said a radar signal “typical of an unmanned aerial vehicle” had been detected in Belarusian airspace. Vilmantas Vitkauskas, the head of the National Crisis Management Centre, said a drone had been spotted in the Vilnius area.

“Based on the parameters we saw, it’s most likely either a combat drone or a drone designed to deceive systems and lure targets,” Vitkauskas said. “The electronic countermeasures here can’t tell us whether an explosive device detonated or not.”

Lithuania’s defence minister, Robertas Kaunas, said the drone had come from Latvia and that it was not known whether it had crashed or left Lithuania’s airspace. Nato fighter jets had been unable to locate it, authorities said.

Russia’s ambassador to the UN caused outrage on Tuesday by claiming Kyiv would soon launch drones at Russia from the Baltic states and telling Latvia that Nato membership would “not protect you from retaliation”.

Lithuania’s foreign minister, Kęstutis Budrys, on Tuesday accused Moscow of “deliberately redirecting Ukrainian drones into Baltic airspace while waging smear campaigns” against all three Baltic states.

Dmitry Peskov, the Kremlin spokesperson, said on Wednesday that Russia’s military was “closely monitoring the situation” regarding drones flying through the Baltic states’ airspace, and was formulating an appropriate response.