The Dutch foreign ministry said it would ask Russia to explain the incident.
Both reported attacks occurred as Moscow and the Hague were already at odds over the Russian state's detention of Greenpeace activists, including two Dutch citizens.
The Dutch diplomat said attackers broke into his apartment late on Tuesday, hit him and drew a heart containing the letters LGBT (lesbian, gay, bisexual, and transgender) on his wall.
He was slightly injured and Russia's ambassador to the Hague had been summoned. Dutch Prime Minister Mark Rutte called the incident "very serious".
Russia's foreign ministry expressed regret over the attack and said it would track down the culprits.