Friday incident, described by Estonia's top diplomat as an "unprecedentedly brazen" incursion, happened just over a week after NATO planes downed Russian drones over Poland, heightening fears that Moscow's war on Ukraine could spill over.
In an online statement published early on Saturday, Moscow stressed its fighter jets had kept to neutral Baltic Sea waters more than three kilometres from Estonia's Vaindloo Island in the Gulf of Finland.
"On September 19, three MiG-31 fighter jets completed a scheduled flight from Karelia to an airfield in the Kaliningrad region," it said, referencing the Russian enclave sandwiched between Polish and Lithuanian territory.
"The flight was conducted in strict compliance with international airspace regulations and did not violate the borders of other states, as confirmed through objective monitoring," the statement said without providing details about the monitoring operation.
With tensions already high because of the war in Ukraine, the incursion came just more than a week after more than 20 Russian drones entered Polish airspace on the night of September 9-10.
Tallinn said the three MiG-31 fighter jets entered Estonian airspace without permission on Friday and stayed for 12 minutes before they were forced to withdraw, during which time the high-speed aircraft could have traversed broad swaths of the country.
"Russia has violated Estonian airspace four times already this year, which is unacceptable in itself, but today's violation, during which three fighter jets entered our airspace, is unprecedentedly brazen," Foreign Minister Margus Tsahkna said.
US President Donald Trump said he had not been briefed on the incident but expected he would be later.
"I don't love it. I don't like when that happens," Trump told reporters when asked if he saw the incursion by Russian jets as a threat to NATO.
"Could be big trouble. I'll let you know later."
Trump's administration is being closely watched for a response after it had little to say about the drone incursion into Poland, triggering anxiety among NATO members, who have questioned Trump's commitment to their defence in case of a Russian attack.
NATO said the incident "is yet another example of reckless Russian behaviour", but a spokesperson on X said it also showed NATO's ability to respond.
Estonia said it had summoned the top Russian diplomat in the country to lodge a protest.
Estonian Prime Minister Kristen Michal said his country would ask NATO to open consultations under Article 4 of the alliance's treaty, and that the Russian jets flew about 9km into NATO airspace before Italian F-35s, stationed at a base in Estonia, pushed them out.
On the battlefront, Russia unleashed a major drone and missile attack on Ukraine overnight, killing three people, injuring dozens more, and damaging infrastructure and residential buildings, President Volodymyr Zelenskiy said.
Despite diplomatic efforts to find ways to end the war that began when Russia invaded in February 2022, the fighting has intensified in recent months.
In a statement on the Telegram app, Zelenskiy said Russia had launched around 580 drones and 40 missiles targeting infrastructure, civilian manufacturing companies and residential areas in different parts of the country.
Air defences shot down 552 of the drones and 31 missiles, Ukraine's air force said.
"All night, Ukraine was under a massive attack by Russia," Zelenskiy said. "Every such strike is not a military necessity but a deliberate strategy by Russia to terrorise civilians and destroy our infrastructure."
Russia denies targeting Ukrainian civilians.
In the central city of Dnipro, a missile with a cluster munition hit a residential apartment building, Zelenskiy said.
One person was killed, and at least 26 people were injured in Dnipro, regional officials said. Two people were also killed in the Chernihiv region in the north and the Khmelnytskyi region in the west of the country, regional officials said.
Reuters could not independently verify the battlefield reports.
with PA