The ministry said the Russian plane was intercepted Wednesday evening after it flew into international airspace north of Estonia and Lithuania without giving a flight plan. The F-16s escorted the plane out of the Baltic airspace.
In Moscow, the Russian Defense Ministry said an Il-76 military transport plane flew from the northwestern city of Pskov to Russia's westernmost Kaliningrad exclave over the Baltics in "strict accordance with international rules of using airspace."
Dutch F-16s taking part in NATO's Air Policing Task Force are based in Malbork, Poland. Wednesday was the first time they have been scrambled to intercept a plane.
Last month, the Western military alliance reported an "unusual" spike in Russian military flights over the Black, Baltic and North seas and the Atlantic Ocean over two days in late October.
Alliance military spokesman Lt. Col. Jay Janzen said on Oct. 29 that four groups made up of Tu-95 Bear H strategic bombers, MiG-31 fighters and other Russian warplanes had been conducting large-scale maneuvers in international airspace.
Tensions have been running high between NATO and Moscow since Russia annexed the Crimean Peninsula from Ukraine in March.
According to NATO officials, alliance pilots have conducted more than 100 intercepts of Russian aircraft this year alone, or about three times more than in 2013.