"The United States cannot blame others... for the consequences of its illegal presence in Iraq and the nation's reaction to the assassination and killing of Iraqi commanders and fighters," foreign ministry spokesperson Abbas Mousavi said.
"Instead of dangerous actions and baseless accusations, Mr Trump should reconsider the presence and behaviour of his troops in the area," he added.
The statement was issued hours after the Pentagon said the US had launched strikes against the Kataeb Hezbollah armed faction.
US retaliatory strikes underway in Iraq: US officials
The United States said the strikes targeted five weapons facilities across Iraq.
It said they were carried out in response to the killing on Wednesday of two Americans and a Briton in a rocket attack on Taji air base.
Wednesday's attack was the 22nd on US installations in Iraq, including the American embassy, since late October.
While there was no immediate claim of responsibility, Washington has blamed what it says are Iran-backed factions from the Hashed al-Shaabi network, a state-sponsored umbrella group that includes Kataeb Hezbollah, for recent similar violence.
Iran has always denied it backs Iraqi militias.
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