Iraqi Prime Minister Adel Abdel Mahdi has condemned the US air strikes which killed at least 25 members of an Iranian-backed Iraqi militia.
Mr Mahdi said the US action on Sunday had violated Iraq's sovereignty.
The prime minister appeared to suggest that Iraq would now have to review its relationship with the US.
US forces targeted the Kataib Hezbollah militia in retaliation for attacks on bases in Iraq that are used by the US military.
The Americans have fought for years alongside Iraqi government forces in their confrontation with the Islamic State (IS) group
"The prime minister described the American attack on the Iraqi armed forces as an unacceptable vicious assault that will have dangerous consequences," his office said.
Mr Mahdi said he tried to inform militia members of the impending air strike against them.
"American forces acted on their political priorities, not those of the Iraqis," a statement said, adding that such strikes "violate the sovereignty of Iraq".
The attacks "force Iraq to review its relations and its security, political and legal framework to protect its sovereignty", the government added.
The US ambassador in Baghdad would also be summoned to discuss the matter, the Iraqi ministry of foreign affairs tweeted.
"We also stress that Iraq is an independent country, that its internal security is a priority... and it will not be allowed to be a battlefield, a passage to carry out attacks, or a place [to be used] to harm neighbouring countries," it added.
Washington on Monday accused the Iraqi authorities of failing to "protect" US interests.
"We have warned the Iraqi government many times, and we've shared information with them to try to work with them to carry out their responsibility to protect us as their invited guests," a senior US state department official told reporters in Washington.
Several attacks have in recent weeks targeted Iraq bases where Americans are present. The US has blamed the attacks on pro-Iran factions.
Sunday's air strikes in Iraq and Syria against Kataib Hezbollah were in response to the killing of a US civilian contractor.
Weapons caches and command and control centres at five sites associated with the militia were hit, the US said.
Kataib Hezbollah (Brigades of the Party of God) is a powerful Iraqi Shia militia that receives financial and military support from Iran.
Since 2009, the US has designated the group as a terrorist organisation, accusing them of threatening the peace and stability of Iraq.
Iran's influence over Iraq's internal affairs has grown steadily since the US-led invasion that toppled Saddam Hussein in 2003.
It has close links to Shia politicians who are part of the ruling elite, and has backed the Popular Mobilisation, which played a key role in defeating IS.
Protesters in Iraq have accused Iran of complicity in Iraq's failure and corruption. They have set fire to a number of Iranian consulate buildings in the country during the recent wave of protests.