Sanctions include the freezing of funds and other financial assets of the Iranian intelligence ministry and individuals, officials said.
The move places both individuals and the intelligence unit onto the EU's terror list, accusing them of carrying out attacks as part of plots against Iranian opposition figures in Denmark and France.
Iran's Foreign Minister Javad Zarif posted a tweet in response to the sanctions saying that "Europeans, incl Denmark, Holland & France, harbor MEK-who killed 12000 Iranians & abetted Saddam's crimes against Iraqi Kurds-as well as other terrorists staging murder of innocent Iranians from Europe", he said, referring to the exiled Iranian opposition group Mujaheedin-e Khalq.
"Iran's involvement in the assassinations underlines the importance of our investigation of the Iranian regime's intentions", AIVD chief Dick Schoof said in a statement.
Dutch Foreign Minister Stef Blok said on Tuesday that his country's secret service had "strong indications" that Iran was involved in the assassination of Dutch nationals in Almere in 2015 and in The Hague in 2017.
"EU just agreed to enact sanctions against an Iranian Intelligence Service for its assassination plots on European soil".
"The EU and the Netherlands take strong action against Iranian unlawful interference in Europe. If such cooperation is not forthcoming, further sanctions can not be ruled out", Blok added.
The Iranian government has denied any involvement in the killings of the two opponents of the regime.
Tehran has time and again strongly denied any involvement in the purported plots, saying the accusations were merely meant to damage EU-Iran relations amid efforts to save the 2015 deal following Washington's withdrawal.
Samuelsen said that some European Union countries were "hesitant" Tuesday about the move due to the nuclear deal with Iran. The latter was dissident Iranian Arab activist Ahmad Mola Nissi who was gunned down by an unidentified assailant in front of his home in The Hague.
The Danish Foreign Ministry named the two employees as the deputy minister and director general of intelligence, Saeid Hashemi Moghadam, and Assadollah Asadi, a Vienna-based diplomat.
France previous year imposed sanctions on two suspected Iranian agents and others from Iran's ministry of intelligence and security.
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Sanctions on the intelligence ministry, which is under the control of Supreme Leader Ayatollah Ali Khamenei, are unlikely to change what the European Union says are Iran's destabilising activities in Europe and the Middle East. "The newly imposed sanctions offer some hope that a growing number of countries are willing to take an active, clear stand against Iran's global campaign of terrorism".
"Iran was informed that involvement in such matters is entirely unacceptable and must be stopped immediately. further sanctions can not be ruled out", a separate statement by the group of European countries imposing the sanctions read.