The incident comes just over a week after more than 20 Russian drones entered Polish airspace on the night of September 9-10, prompting NATO jets to down some of them and member countries' officials to say Russia was testing the alliance's readiness and resolve.
The airspace violation comes three days after Russian and Belarusian military forces ended joint military exercises, called Zapad 2025.
Officials in Tallinn said on Friday the three MiG-31 fighter jets entered Estonian airspace without permission and stayed there for a total of 12 minutes.
"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.
"Russia's ever-increasing testing of borders and aggressiveness must be responded to by rapidly strengthening political and economic pressure."Â
The Russian Defence Ministry did not immediately respond to a request for comment.
Estonia said it had summoned the top Russian diplomat in the country to lodge a protest and deliver a note.
Estonian Defence Forces said the airspace violation occurred on Friday morning in the area of Vaindloo Island, about 100km from the capital Tallinn.
The aircraft did not have flight plans, their transponders were not switched on and they were not in contact with air traffic control, Estonia said.
While incursions over Vaindloo Island by Russian aircraft are fairly common, they do not usually last as long as Friday's incident.
"This could be a test by Russia to see how NATO responds to this type of challenge but it could also be purely coincidental," Jakub M Godzimirski, a research professor in Russian security policy at the Norwegian Institute of International Affairs, told Reuters.
"Still, this happens in a given context, having in mind what happened with the drone incursion in Poland a few days ago."
Ukrainian First Deputy Foreign Minister Sergiy Kyslytsya said on Friday the country was making progress in intensive talks to formalise legally binding security guarantees with the United States and European allies.
A bilateral agreement with the United States remains vital and US President Donald Trump's recent commitment to participate in Ukraine's defence was a "breakthrough moment," Kyslytsya told Reuters in an interview.
"I think that we are making progress," said Kyslytsya, a key negotiator with allies on security guarantees who also participated in all three rounds of direct talks with Russia in Istanbul earlier this year.
"I think this very intense period of exchange of views allows us to have a much better and concrete understanding of who is willing to do what and who is capable of doing what."
Kyslytsya said the vast majority of about 30 countries in the so-called "coalition of the willing" promising support for Ukraine had offered practical help, although details were still being thrashed out.
Ukrainian officials have said proposals under discussion as part of security guarantees include a strong well-equipped Ukrainian army, foreign troops on the ground, finance for domestic and overseas weaponry and intelligence sharing.
The aim is to create a credible deterrent against future Russian aggression, although participating countries differ widely in what they are prepared to contribute and Kyslytsya said that more progress needs to be made.
He said there was still a decision to be made on whether Ukraine would have a set of bilateral treaties with its European allies or a multilateral agreement among several countries.
After more than three-and-a-half years of war, polls show increasing exhaustion in Ukraine and support for a potential ceasefire but there remains overwhelming opposition to Russian demands to give up occupied land and to cede yet more territory.
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