The EU imposed sanctions on Tehran over the killings.
Foreign Minister Stef Blok said in a letter to parliament that the government "has decided to recall the Netherlands' ambassador to Tehran for consultations" over the row.
Iran's decision to expel the Dutch officials – which was not previously announced in public – was "not acceptable and is negative for the development of the bilateral relationship", Blok said.
He said Iran's move was itself a tit-for-tat response to the Netherlands' expulsion of two Iranian embassy workers in June 2018 "due to strong indications from the Dutch intelligence services that Iran has been involved in the liquidations on Dutch territory of two Dutch people of Iranian origin".
Iran informed Dutch authorities of the decision to expel the two on 20 February and they were deported back to the Netherlands on Sunday, Blok said.
The Dutch also summoned the Iranian ambassador over the issue.
Netherlands police have previously named the two murder victims as Ali Motamed, 56, who was killed in the central city of Almere in 2015, and Ahmad Molla Nissi, 52, murdered in The Hague in 2017.
Hafte Tir bombardment
But Dutch newspaper Parool reported last year that “Ali Motamed,” an electrician who lived in Almere, received a Dutch residence permit in the early 1990s and was murdered on 15 December 2015, was “very probably” Mohammed Reza Kolahi Samadi.
Samadi is blamed by Iran for organising the 1981 Hafte Tir bombing of the headquarters of the Iran Islamic Republic Party in which 73 leading officials, including chief justice Ayatollah Mohammad Beheshti, lost their lives.
The paper says, without naming a source, that “Motamed” was a member of the Mujaheddin-e-Kalq (People’s Mujaheddin or MEK, a Paris-based opposition group) and came to the Netherlands in “the '80s”.
He was sentenced to death in absentia in Iran, and was “wanted internationally”.
Motamed was married to a Dutch wife with whom he had a son. Two Amsterdam-based criminals, Anouar A.B. and Moreno M. are suspected of the murder.
They appeared in court on 25 May, 2018.
The incident comes at a time when Iran is attempting to salvage the 2015 Joint Comprehensive Plan of Action, the “nuclear deal” between Iran and the five permanent members of the UN Security Council and Germany.
The deal is in danger after the US unilaterally walked away from it and re-instated sanctions, saying the plan was not sufficient to prevent Iran from developing nuclear weapons.
Russia and China said they will stick to the deal. The three other signatories, France, the UK and Germany have created a channel for non-dollar trade with Iran to avoid US sanctions.