LONDON — The European Union penalized Iran on Tuesday over allegations that the country’s intelligence service orchestrated a series of assassination plots in Europe in recent years, including the killing of two Iranians in the Netherlands with ties to anti-government extremist groups.
In a letter outlining its justification for sanctions, the Dutch Foreign Ministry cited “strong indications that Iran was involved in the assassinations of two Dutch nationals of Iranian origin,” one in 2015 in the city of Almere and another in 2017 in The Hague.
European intelligence officials have also linked the Iranian government to unsuccessful plots in Denmark and France.
“In the Dutch government’s opinion, hostile acts of this kind flagrantly violate the sovereignty of the Netherlands and are unacceptable,” the letter said.
The sanctions were imposed under steps devised by the European Union to combat terrorism after the Sept. 11, 2001, attacks in the United States. They involve freezing assets connected to Iran’s Ministry of Intelligence and Security and two Iranian officials: Saeid Hashemi Moghadam, a senior Iranian intelligence official, and Assadollah Asadi, an Iranian diplomat arrested in connection with a plot to bomb a rally of an Iranian opposition group in Paris last year, according to officials familiar with the sanctions.
Iran has long been suspected of covertly carrying out violence against opponents living outside its borders. In remarks delivered shortly after becoming secretary of state last year, Mike Pompeo accused Iran’s elite Revolutionary Guards force of conducting “covert assassination operations in the heart of Europe.”
But it is unusual for the 28-member European Union to confront such an issue so directly.
On Tuesday, ambassadors from Belgium, Britain, Denmark, France, Germany and the Netherlands visited the Iranian Foreign Ministry in Tehran “to convey their serious concerns” about Iran’s behavior, according to the Dutch letter.
In response, Iran’s foreign minister, Mohammad Javad Zarif, did not deny the allegations, but accused European countries in a Twitter post of harboring militants from the Mujahedeen Khalq, or M.E.K., a group that seeks the violent overthrow of the Iranian government.
M.E.K., designated as a terrorist group by the United States until 2012, has been praised by John R. Bolton, President Trump’s national security adviser, and Rudolph W. Giuliani, the president’s personal lawyer and former New York mayor.
“Accusing Iran won’t absolve Europe of responsibility for harboring terrorists,” Mr. Zarif wrote.
The decision to impose sanctions underscores the difficult balancing act facing the European Union as it tries to counter suspected Iranian misbehavior and preserve the Iran nuclear accord.
Under that accord, reached in 2015, Iran is supposed to receive economic incentives in exchange for verifiable promises of peaceful nuclear work.
The Trump administration, which withdrew the United States from the accord last year and reimposed tough sanctions on Iran, has pressured Europe to adopt a similarly hard line. The Europeans have so far resisted, vowing to create ways for companies to circumvent American sanctions.
In its letter, the Dutch Foreign Ministry said the European Union would treat the assassination plots and the nuclear accord as separate issues. But that position could become increasingly untenable. If Iran’s suspected misbehavior persists, Europe could be forced to come into alignment with the United States, said Sjoerd Sjoerdsma, a Dutch member of Parliament.
“I think ultimately that would not be a good thing,” he said, “but it’s up to Iran to make sure that that doesn’t happen.”
The two Iranian nationals killed in the Netherlands were tied to groups accused by Iran’s government of involvement in violence. In December 2015, the body of Ali Motamed, 56, was discovered in the street in front of his house in Almere. He had been living in the Netherlands since the 1980s, had obtained Dutch citizenship and had been working as an electrician.
The Dutch authorities later determined that Mr. Motamed was actually Mohammad Reza Kolahi Samadi, an M.E.K. member sentenced by Iran to death for involvement in a 1981 bombing that killed 73 people in Tehran.
His death was followed a few years later by the fatal shooting of Ahmad Mola Nissi in The Hague. Mr. Mola Nissi was the leader of the Arab Struggle movement for the liberation of al-Ahvaz, an armed Iranian opposition group accused of carrying out several bomb attacks in Iran, including an attack on a military parade in September that killed at least 25 people.
In response to the killings, the Dutch government expelled two Iranian diplomats in June last year.
The European authorities thwarted several planned attacks on opponents of the Iranian government beginning last summer. In June, police officials from France and Belgium disrupted a plot to bomb a rally organized by a Paris-based group dominated by the M.E.K. The rally was attended by Mr. Giuliani and Newt Gingrich, a former House speaker. A Belgium couple of Iranian origin were arrested in connection with the plot, along with Mr. Asadi, the Iranian diplomat.
Mr. Asadi, based in Vienna, was an officer of the Iranian Intelligence Ministry who used the alias Daniel, said a senior Middle Eastern intelligence official, who spoke on the condition of anonymity to discuss a continuing intelligence operation. He was detained by Germany’s antiterrorism police and extradited to Belgium.
In November, Denmark’s government accused Iran of trying to assassinate the head of the local branch of the Arab Struggle Movement, which seeks an independent state in Iran’s oil-rich Khuzestan Province. A Norwegian man of Iranian descent was arrested, prompting a congratulatory Twitter post from Mr. Pompeo.
The Mossad, Israel’s intelligence agency, provided the tip that led to the disruption of the plots, the senior intelligence official said.