"Based on police information, Foreign Minister Frans Timmermans comes to the conclusion that the detention of the Russian diplomat... Breached the Vienna Convention," ministry spokesman Thijs van Son said in an email.
"Because of this the Netherlands apologises to the Russian Federation," it said, adding however that police had acted out of professional responsibility when detaining diplomat Dmitry Borodin.
Russian President Vladimir Putin yesterday called Borodin's detention at a police station for several hours on Saturday night "the most gross breach of the Vienna Convention", and demanded an apology.
"At the same time Minister Timmermans personally understands the behaviour of the police involved, who acted out of professional responsibility when confronted with a situation that they discovered after being called," the statement said.
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"The Netherlands and Russia remain in contact over the further resolution of this incident."
Ties between Russia and the Netherlands have deteriorated sharply since Russian investigators last week charged 30 crew members of a Dutch-flagged Greenpeace ship, the Arctic Sunrise, with piracy over a protest against Arctic oil drilling.
The Russian foreign ministry yesterday accused Dutch police of raiding Borodin's apartment in The Hague and beating him up before taking him to a police station for hours of questioning on accusations of mistreating his children.
The Vienna Convention on Diplomatic Relations grants diplomats immunity from arrest.