"The foreign ministry presented an official letter of protest to the Iranian ambassador in Baghdad over Iranian forces' bombardment of border villages on Iraqi territory," it said in a statement.
It went on to demand an "immediate halt to these sorts of violations which continue to have negative repercussions on relations between the two countries."
"While Iraq understands the Iranian authorities' motivation to secure its borders, it will not be achieved by unilateral actions, but by bilateral contacts and constructive dialogue."
Iraq's Kurdish regional government lodged a similar protest following the raid on Saturday in which Iranian helicopters strafed three Kurdish villages in Tehran's first aerial raid against Kurdish rebels.
No one was reported killed or wounded in the assault.
The regional government called on Kurd separatists to end all attacks on Turkey and Iran, which share rugged, mountainous borders with Iraq from where the groups stage their incursions.
The rebels' remote hideouts have come under frequent bombardment by Turkey and Iran in past months.
The aerial raid appeared to have targeted the Party of Free Life of Kurdistan (PJAK), an Iranian Kurdish separatist group which has launched attacks on Iran from rear-supply bases in the mountains of northern Iraq.
The group is closely allied with the Kurdistan Workers' Party (PKK), which has launched similar attacks against Turkey.
Blacklisted as a terror group by the European Union and the United States, the PKK took up arms for self-rule in Turkey's Kurdish-majority southeast in 1984, triggering a conflict that has claimed some 44,000 lives.
Iraq, Iran, Syria and Turkey all have significant ethnic Kurdish minorities.
Tehran and Baghdad fought a devastating 1980-1988 war in which around one million people died, but ties have warmed considerably in the wake of the 2003 US-led invasion that toppled the Iraqi dictator Saddam Hussein.
