Speaking after a Baghdad cabinet meeting on Tuesday, Iraqi government spokesman Ali al-Dabbagh also explicitly criticised the US over the unconfirmed helicopter strike.
"The Iraqi government rejects the US helicopter strike on Syrian territory, considering that Iraq's constitution does not allow its land to be a base for launching attacks on neighbouring countries," he said.
But he urged Damascus to prevent groups using Syrian territory for "training and sending terrorists for attacks on Iraq and its people".
The White House has neither confirmed nor denied Sunday's strike near Abu Kamal, some eight kilometres (five miles) north of Iraq's border with Syria.
Syria had protested to the UN Security Council in a letter to Secretary General Ban Ki-moon, the state news agency Sana said on Tuesday.
It urged the Security Council "to hold the aggressor responsible for the deaths of the innocent Syrian nationals".
An unnamed US official told Reuters news agency the raid killed Iraqi Abu Ghadiyah, a former lieutenant of Abu Musab al-Zarqawi, the al-Qaeda in Iraq leader who was killed in 2006.
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