The all-Filipino advance party were paving the way for a US team to set up development projects in a village near the town of Tuburan on Basilan island, officials said.
The firefight erupted after five gunmen believed to be linked to the Abu Sayyaf opened fire on the aid workers and their escorts on Sunday, a military report said.
No reason was given for the delay in releasing the report.
One gunman, identified as Sabbadin Sabudin, was killed while another was wounded, the report said. There were no casualties on the government side and among members of the aid workers.
Reports reaching the Armed Forces Southern Command here said two platoons of Army soldiers were escorting the local team when they were fired upon in Tuburan.
The local contractors who won the bid are conducting the projects that are part of the humanitarian projects of the US forces in Basilan.
A small group of US military advisers are pursuing humanitarian work on Basilan – such as road and bridge building – after a six-month joint anti-terrorism operation with Filipinos ended in July.
The operation, known as Balikatan 02-1, resulted in the death of an Abu Sayyaf leader and an American hostage and the rescue of another captive from the United States.
Capt. Catherine Olivera, spokeswoman for the US Joint Task Force 510, said no US troops were involved in the incident Sunday and neither was there any American in the team that conducted the survey.
"That report (gunmen firing at US medical team) is incorrect," Olivera said. "It is the soldiers of the host nation who are involved," she added when asked if there were US troops in the area.
Basilan information officer Cris Puno said apart from Basilan, a contingent of US forces were also left behind in Zamboanga City to monitor their projects being implemented by local contractors.
The projects include water wells, school houses, hospital and barangay health centers funded by the US government under the Balikatan.
The other day, the Abu Sayyaf tried to destroy some deep well projects of the US engineering brigade in Sumisip town, but an alerted paramilitary unit foiled the plan.
Security around Basilan schools was meanwhile tightened after the Abu Sayyaf threatened to abduct teachers and students in retaliation for the deaths of four rebels in a military offensive on Monday.
Provincial spokesman Alton Angeles said the threat was contained in an intelligence report submitted to the office of Basilan Governor Wahab Akbar.
"The rebels are now threatening to seize our teachers in retaliation for the killing of four of their companions," Angeles told local radio here.
He did not divulge other details of the intelligence report, although the Muslim Abu Sayyaf group described as terrorists by the United States has in the past targeted Muslim teachers and students in Basilan.
Two years ago, Abu Sayyaf gunmen seized a priest and more than 50 students and teachers from a Roman Catholic school in Basilan. Two male teachers were beheaded, while the priest was shot dead after being tortured. The other victims were either freed or rescued in batches.
"We have deployed soldiers in Basilan and tightened security in many areas to prevent the rebels from harassing civilians," Basilan army commander Col. Bonifacio Ramos said.
The Abu Sayyaf is a small group of Islamic militants linked by Manila and Washington to the al-Qaeda network led by suspected terrorist mastermind Osama bin Laden. The Abu Sayyaf are however more notorious for their kidnapping sprees.
Meanwhile, in Zamboanga City, reports said Armed Forces chief Gen. Benjamin Defensor has sent three more bombers to Sulu to provide air cover to troops running after the Abu Sayyaf.
The military has predicted that the bandits would be neutralized within six months.
Lt. Gen. Ernesto Carolina, Armed Forces Southern Command chief, said the bombers landed Saturday at Edwin Andrews Air Base here from Sangley Point in Cavite.
"The SF-260s are trainor planes converted into Marquette bombers, and was also utilized during the Cabatangan Complex siege in Zamboanga City by the followers of jailed Muslim leader Nur Misuari last November 27," he said.
"The Chief of Staff sent three additional bomber planes to augment our air attack in the Operation Endgame. There will be a mix of air attack assets that will be utilized in the operation against the bandits in Sulu."
Carolina said the warplanes have been placed on standby while troops are pushing the bandits to constrict them to a "target spot," where they could be bombed. — With Roel Pareño, Paolo Romero