Tehran summoned the Dutch ambassador and the Islamic Republic protested at the deportation of two Iranian diplomats in the Netherlands, the Iranian foreign ministry spokesman was quoted as saying by IRNA on Saturday.
A European government official and a Western intelligence source said on Friday that the expulsions of two Iranian embassy staff occurred up to two months ago.
The Iranian foreign ministry Bahram Qasemi did not say when the ministry's meeting with the Dutch ambassador took place.
He said the deportation of Iranian diplomats was "unfriendly and unconstructive" and said Iran has the right to take reciprocal measures.
"Instead of expelling Iranian diplomats, the Dutch government should explain why it has harboured members of a terrorist organisation," Mr Qasemi said, mentioning the People's Mujahideen Organization of Iran. That group is linked to the Paris-based National Council of Resistance of Iran - a bloc of opposition groups in exile that seek an end clerical rule in Iran.
The group, also known by its Persian name Mujahideen-e-Khalq, was once listed as a terrorist organisation by the United States and the European Union but is not any more.