Russia's defence ministry denied its jets violated Estonian airspace, saying they flew over neutral waters.
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.
That prompted NATO jets to down some of them and Western officials to say Russia was testing the alliance's readiness and resolve.
It also occurred three days after Russia and Belarus ended their "Zapad-2025" joint military exercises, which included the rehearsal of the launch of Russian nuclear weapons.
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.
Russian jets routinely fly over the Baltic Sea between mainland Russia and its exclave of Kaliningrad.
The Russian defence ministry on Saturday said its jets flew over neutral waters of the Baltic Sea in proceeding from northwest Russia to Kaliningrad.
"The flight was carried out in strict conformity with international rules governing airspace with no violation of the borders of other states as is confirmed by independent checks," the ministry posted on Telegram.
"The Russian aircraft did not deviate from the agreed flight path and did not violate Estonian airspace."
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.
Europeans quickly responded to the Russian jet incident on Friday, with EU foreign policy chief Kaja Kallas - a former Estonian prime minister - saying: "This was no accident."
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.
Ukraine called the incursion an unacceptable new destabilisation measure by Russia and said it stood with Estonia.
"Strong action is needed, both jointly and from individual countries," President Volodymyr Zelenskiy said on the Telegram messaging app.
Estonia said the airspace violation occurred on Friday morning in the area of Vaindloo Island, about 100km from the capital, Tallinn.
Separately, Polish and allied aircraft were deployed early on Saturday to ensure the safety of Polish airspace after Russia launched air strikes targeting western Ukraine near the border with Poland.
"Polish and allied aircraft are operating in our airspace, while ground-based air defence and radar reconnaissance systems have been brought to the highest state of readiness," the operational command said in a post on X.
Shortly after 3pm AEST, Polish and allied air forces ended the operation as air strikes by the Russian Federation against Ukraine were ceased, the Polish command said, adding the actions were "preventative and aimed at securing airspace in areas adjacent to the threatened area".
