The Russian ambassador was summoned by the Dutch foreign ministry to explain the incident.
The diplomat, Onno Elderenbosch, 60, was lightly injured in the attack, which saw him bound and his apartment ransacked.
The attackers scrawled the words "LGBT" on his mirror before leaving without stealing anything.
They also drew a heart in pink lipstick.
More from GlobalPost: Bail denied for US Greenpeace ship captain in Russia hearing
Tensions between Moscow and the Hague have been high after Russia detained a Dutch-flagged Greenpeace ship carrying activists who attempted to board a Gazprom oil platform in the Arctic.
The Netherlands launched legal action against Russia, saying that the activists have been unlawfully detained.
Two of the activists are Dutch citizens.
Police in the Hague detained a Russian diplomat last week after he was accused of abusing his children.
He was quickly released and the Dutch government apologized for violating the Vienna Convention on diplomatic relations, which grants the man immunity.