A Russian Su-27 fighter was detected in the Gulf of Finland south of Porvoo late on Thursday, the ministry said.
Another Russian Su-27 was detected on a suspicious flight there earlier. "Russian military aviation over the Baltic Sea has been intense," it said.
The Russian military said there was no violation of Finnish airspace.
The Russian defence ministry said "the flights took place over neutral waters in the Gulf of Finland" and "no plane deviated from its set course".
The Su-27s were flying in the area for training purposes, it added.
Just hours after the incidents, Finland signed a defence co-operation pact with the US. It is a non-binding commitment to boost military information-sharing, joint training, research and defence against nuclear and other non-conventional threats.
The "statement of intent" was signed in Helsinki by US Deputy Secretary of Defense Robert Work and Finnish Defence Minister Jussi Niinisto.
Finland is not in Nato but co-operates closely with the 28-nation alliance.
Porvoo lies just east of Helsinki, and is 140km (87 miles) from the Russian border.
Nato has complained repeatedly of provocative Russian military flights in the Baltic region. But it is rare for Finland to report such suspected violations.
Russian bombers also regularly fly long patrol missions from the Arctic down to the North Atlantic or Bay of Biscay, testing Nato reactions on the way.
And Russia plans to step up similar patrols in the North Pacific, sending bombers from bases in eastern Siberia.
Russia was angered by the deployment of Nato forces in the three Baltic states - Estonia, Latvia and Lithuania - after those nations broke away from the Soviet Union in 1991 and joined Nato in 2004.
During the Cold War - which ended in 1991 - Finland remained neutral and developed strong trade ties with the Soviet Union.
Finland's Defence Ministry says it has scrambled jets twice in the past 24 hours to monitor suspected airspace violations by Russian fighters.