Col. Alexander Aleo, commander of the Philippine Armys 103rd Infantry Battalion, said there were no immediate reports of casualties on either side.
It was the first incident of direct combat between the US troops and the Abu Sayyaf bandits who still hold hostage American missionary couple Martin and Gracia Burnham and Filipino nurse Deborah Yap in their jungle lair in Basilan.
Both Philippine and US authorities believe that the Abu Sayyaf is linked to the al-Qaeda network of Saudi dissident Osama bin Laden.
About 1,000 US soldiers are deployed in Basilan and nearby Zamboanga City to train and advise Filipino troops tracking down the Abu Sayyaf bandits.
The Americans are not allowed to participate in actual combat, but can fire back in self defense.
Initial reports reaching the militarys Southern Command headquarters in Zamboanga City said that the two choppers were flying low over the treetops when about 10 suspected Abu Sayyaf gunmen fired at the aircraft.
The helicopters fired back, sending the rebels scampering for safety.
"It was not a hostile fire. It was a coordinated exercise. They (helicopters) fired blanks," said Maj. Richard Sater, spokesman for the US contingent code-named US Joint Task Force 510.
"Reports that two US air force helicopters exchanged hostile fire with ground troops on Monday are incorrect," Sater said.
He said two US Army MH-47 Chinook helicopters were conducting "coordinated aerial demonstration on Monday night on the north and eastern shores of Basilan."
At the same time, Sater said the US and Philippine forces on the ground set off some incendiary devices to simulate enemy contact. "But at no time was there any live fire exchange or hostile fire from the air or the ground," he said.
Southcom spokesman Col. Fredesvindo Covarrubias, who maintained earlier that it was an attack by Abu Sayyaf members as the helicopters were flying above the treetops of Tuburan, admitted later there was an error in their report.
"We cannot prevent attacks. These are indiscriminate acts by terrorists," Covarrubias had said.
"We are going to take extra precautions and additional security patrols in areas of training," he added.
Meanwhile, US Deputy Defense Secretary Paul Wolfowitz is expected to arrive in Manila this week as part of his Asian tour meant to discuss Washingtons global war on terrorism with leaders of the region.
Wolfowitz will also attend and speak at an Asian security conference sponsored by the International Institute of Strategic Studies in Singapore on June 1 and 2.
Pentagon spokeswoman Victoria Clarke said Wolfowitz would stop in the Philippines on his way home to visit the US troops in Mindanao.
A former ambassador to Indonesia, Wolfowitz is considered an expert on Asia-Pacific affairs and has maintained a strong interest in the region while serving as a senior official in both the State and Defense departments. Paolo Romero, AFP