The Russian Foreign Ministry announced on Monday that they had "strongly protested" to the discovery of "tracking equipment" in the service car of an embassy assistant.
Moscow has instructed the Charge d'Affaires of the Netherlands, Dominique Bakker-Kühling, to "immediately take comprehensive measures to prevent such incidents".
"Such unfriendly actions complicate the already difficult bilateral relations," the ministry said in a statement.
Prime Minister Mark Rutte has declined to comment, according to Dutch media.
Espionage cases have increased in recent years between Russia and the West, with whom relations are at their lowest since the Ukrainian crisis and Moscow's annexation of the Crimean peninsula in 2014.
In 2018, Dutch authorities said they had disrupted an attempted hack on the office of the Hague-based Organization for the Prohibition of Chemical Weapons (OPCW).
According to the Dutch military intelligence service, the hack was committed by four Russian secret service officers, who had travelled to the Netherlands with diplomatic passports.
Russia then dismissed the claims as allegations by someone with a “rich imagination”.