According to an official statement, an AN-12 military transport plane on route to the Russian Baltic exclave of Kaliningrad flew about 3km into Estonian airspace near the island of Vaindloo, remaining there for about a minute.
Russian Navy official Igor Dygalo said preliminary data did not confirm a violation has occurred.
"The information about a possible violation of Estonian airspace by a Russian military plane is being checked," he said.
This is not the first time a Russian military aircraft has been charged with violating Baltic airspace in recent months.
In a highly publicized case in September, a Su-27 Flanker fighter from the 6th Air Army was flying from St. Petersburg to Kaliningrad when it crashed on Lithuanian territory. Russia compensated Lithuania with about 19,500 euros for damages caused by the crash.