The Ilyushin IL-20 "intelligence collection aircraft", which took off from the Russian Baltic coast enclave of Kaliningrad yesterday, was first intercepted by Danish F-16 jets when it approached Denmark, NATO said in a statement.
It then flew north towards non-NATO member Sweden which also sent jets to intercept the plane.
Nearly four hours later the plane flew towards NATO member Estonia and was detected in Estonian airspace "for a period of less than one minute, which represented an incursion of about 600 metres (yards) into NATO airspace," it said.
The Ukraine crisis has produced the worst east-west tension since the end of the Cold War.
NATO has stepped up its Baltic air patrols due to what it says is a surge in intercepts of Russian warplanes near Polish and Baltic airspace since Moscow's annexation of Crimea from Ukraine in March.
The Swedish Navy meanwhile has been searching for a suspected Russian submarine off the coast of Stockholm for nearly a week, although it said today it was pulling back some of its ships.