Iraqi government spokesman Ali al-Dabbagh said Baghdad was "in contact with the American side about reports regarding the attack along the frontier with Syria".
But he added that the attacked area "is a theatre of insurgent activities against Iraq using Syria as a launch pad".
Neither the Pentagon nor the White House has made any official comment. A US military spokeswoman in Baghdad said it was "in the process of investigating".
Syria's press attache in London, Jihad Makdissi, told the BBC the incident was "an outrageous crime and an act of aggression".
"If [the US has] any proof of any insurgency, instead of applying the law of the jungle and penetrating, unprovoked, a sovereign country, they should come to the Syrians first and share this information," he said.
Mr Makdissi said the US government had "proved to be irrational and they have no respect for international law or human rights".
He warned that Syria would "respond accordingly in the proper way".
The government newspaper Tishrin called the act a "war crime".
They started firing at us. My little boy ran out and as I went to protect him they shot me
Wife of a security guard
Although there has been no official US response, an unnamed US military official told the Associated Press news agency that special forces had targeted al-Qaeda linked militants moving across the border.
"We are taking matters into our own hands," the US official said.
The official said there had been considerable success closing lines of entry for foreign militants but added: "The one piece of the puzzle we have not been showing success on is the nexus in Syria."
Several days ago the commander of US forces in western Iraq said they would be increasing operations to secure the border as it had become an "uncontrolled" entry point for militants.
US intelligence believes up to 90% of the foreign fighters entering Iraq come through Syria.
Syria's official Sana news agency said that "four American helicopters violated Syrian airspace around 1645 local time [1345 GMT] on Sunday".
"We were at the building site when four [soldiers] came down. Four [soldiers] headed towards us and another four went towards the workers who were putting in the foundation concrete," a woman identified as the wife of a security guard told Syrian television.
"They started firing at us. My little boy ran out and as I went to protect him they shot me. There were four aircraft - two of them landed while the other two remained airborne. The aircraft also kept on firing at us. They killed the workers. When I went to catch my son they shot me. He was running towards his father."
TV pictures showed a truck riddled with bullet holes and a blood-stained floor.
Our correspondent says the timing of the incident is curious, coming right at the end of the Bush administration's period of office and at a moment when many of America's European allies - like Britain and France - are trying to broaden their ties with Damascus.
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