Netherlands' Defence Minister Ank Bijleveld-Schouten said on Tuesday that Russian fighter jets armed with air-to-surface missiles had harassed a Dutch navy frigate in the Black Sea this month, conducting mock attacks and jamming communications.
The Russian Defence Ministry said it scrambled fighter jets and bombers to prevent the frigate from entering Russian waters, news agencies reported.
The Russian military said the warplanes flew at a safe distance from the vessel and in line with international regulations.
The Netherlands' Defence Ministry said the Russian actions took place over five hours on June 24 and breached rights to free use of the sea.
The frigate, Evertsen, was sailing with Britain's Carrier Strike Group, which was conducting a patrol in the area at the time.
Ms Bijleveld-Schouten called the Russian action "irresponsible".
"The Evertsen has every right to sail there," she said. "There is no justification for this kind of aggressive act, which needlessly increases the chance of accidents."
She said the Netherlands would raise the matter with Russia at the diplomatic level.
A similar incident occurred last week, between London and Moscow, after the HMS Defender passed near Crimea in the Black Sea.
Russia said it fired warning shots at the destroyer to ward it off, but Britain denied the claim.
Russia annexed Crimea from Ukraine in 2014 and claims the water around the peninsula as its territory.
Much of the international community, including Britain, did not recognise the move and stand behind Ukraine's claims to the water.