"They violate our airspace on a fairly regular basis, they fly across the Baltic Sea with the transponders switched off," Hannes Hanso told a small group of reporters on a visit to Paris to meet his French counterpart Jean-Yves Le Drian.
While military radar can detect a plane even when its transponders are switched off, radar designed for civilian aircraft cannot, Hanso said.
"It is incredibly reckless and it is an accident waiting to happen," the minister said.
"Imagine a collision between a Russian plane and a civilian plane.
Baltic countries want a NATO summit in Warsaw in July to send a clear message to Russia, the Estonian minister said.
"We want to make sure that the regime in Moscow gets a very clear message that this sort of behaviour is not acceptable and territories of alliance will be defended no matter what.
"So it is about deterrence."
Relations between NATO and Russia have deteriorated since Russia annexed the Crimea region of Ukraine and eastern European countries are worried that they too might be targets of Russian aggression.
In April, Russian jets deliberately flew low over a US naval destroyer in the Baltic Sea.
Russia claimed the planes were conducting test flights and said the ship was in the vicinity of the Russian navy's Baltic fleet base.
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