"It is not at all acceptable that one of our neighbours that has deep relations with us ... becomes a centre for creating threats against the Islamic republic," said foreign ministry spokesman Saeed Khatibzadeh.

"Iran will not tolerate that a centre near its borders becomes the centre for sabotage, conspiracy and sending terrorist groups to Iran," he said at his weekly press conference in Tehran.

Iran's Revolutionary Guards, the ideological arm of the armed forces, said Sunday they had targeted a "strategic centre" belonging to Israel, the Islamic republic's arch enemy, in the northern Iraqi city of Arbil, using "powerful precision missiles".

Kurdish authorities, however, insisted that the Jewish state has no sites in or near Arbil, the capital of their autonomous region in Iraq's north.

The authorities said a dozen ballistic missiles had targeted Arbil, including some US facilities, in the pre-dawn cross-border attack that lightly wounded two civilians.

Baghdad summoned the Iranian ambassador, Iraj Masjidi, to protest the strikes as Iraq's foreign ministry condemned the attack as a "flagrant violation of (Iraqi) sovereignty".

Khatibzadeh said that the federal government of Iraq "has been notified several times ... not to allow Iraq's borders with Iran to become insecure".

"Iran expects the central government of Iraq to end this situation once and for all and not allow its borders to be abused," he added.

Sunday's attack came nearly a week after two officers of Iran's Revolutionary Guards were killed in Syria in a strike attributed to Israel, a key US ally.

Iraq, including the Kurdistan region, is home to a now reduced deployment of US troops who led a coalition fighting the Islamic State jihadist group.

Washington has blamed a series of rocket and drone attacks against its military and diplomatic interests in Iraq on pro-Iran groups who demand the departure of the remaining US troops, but cross-border missile fire has been rare.