"Nobody has the right to interfere in Iraqi affairs," the Iraqi cabinet said in a statement, quoting a source close to Prime Minister Haider al-Abadi.
"The fighters of the Hashed (al-Shaabi paramilitary units) are Iraqis who are concerned for their country and have sacrificed for its defence and for its people," it said.
Yesterday, US Secretary of State Rex Tillerson demanded that Iranian militias leave Iraq.
"Certainly Iranian militias that are in Iraq, now that the fighting against (IS) is coming to a close, those militias need to go home," Tillerson said.
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The 60,000-strong Hashed was formed in 2014 after IS seized swathes of northern Iraq, routing government forces.
A coalition mostly made up of Iranian-backed militias, it has played a key role in Iraq's successful fightback against the jihadists over the past three years.
It answers to Iraq's prime minister as commander-in-chief of the Iraqi armed forces, into which it has been integrated by a parliamentary vote.
Tillerson's remarks were also aimed at Iran's elite Revolutionary Guards and their foreign operations wing, the Quds Force, according to a senior US official accompanying him.
Iranian Foreign Minister Mohammad Javad Zarif has also hit back at Tillerson's remarks, saying Iran played a crucial role in the fight against IS both in Iraq and Syria.
"If it wasn't for the sacrifices of the Islamic Republic of Iran... Daesh (IS) would have installed its government in Damascus, Baghdad and (the Iraqi Kurdish regional capital) Arbil by now," he said.