The fighting started after Special Action Force troops raided an Abu Sayyaf hideout near the town of Datu Saudi Ampatuan.
Army soldiers reinforced the police as the gunbattle intensified.
Lt. Col. Buenaventura Pascual, Armed Forces public information
chief, said an undetermined number of MILF guerrillas were also wounded in the accidental encounter.
"Before the encounter, Janjalani and at least three companions were sighted in the area," he said. Government troops were about to move in when "they were encountered by the MILF troops under Commander Wahid," he added.
Pascual said troops from the Army’s 64th Infantry Battalion were poised to strike at Janjalani and his companions — suspected Jemaah Islamiyah terrorists — when MILF rebels under Commander Wahid fired at them at about 5:30 a.m. at Barangay Gawang in Datu Odin Sinuat town.
"We can categorize this as a misencounter because the MILF is very cooperative in this effort to get Janjalani," he said.
"The tactics of the (Abu Sayyaf) in Sulu, they are applying it in Maguindanao. They are resting near MILF troops. It’s part of the combat chaos.
"When you are on the ground and when you see an armed group, your tendency is to fight them to defend and protect yourself."
Members of the government’s ceasefire committee are now in Barangay Gawang negotiating with the MILF to pull out its
forces and allow the soldiers to proceed and continue their pursuit of Janjalani and his men.
The government mounted offensives after Abu Sayyaf suspects bombed a passenger ferry at the weekend, injuring 30 people.
On Tuesday, troops captured Hajiri Tadja, a suspected Abu Sayyaf militant who allegedly took part in the kidnapping of Asian and European hostages from a resort off Sabah in 2000.
All the hostages were freed in exchange for huge ransoms, officials said.
Security officials say the Abu Sayyaf has made links with the Jemaah Islamiyah, blamed for the October 2002 bombings in Bali, Indonesia.
Officials earlier warned that up to 10 Indonesian Jemaah Islamiyah militants were plotting suicide attacks in the country with the aid of Abu Sayyaf scouts.
Meanwhile, intense fighting broke out yesterday morning between armed supporters of three Maguindanao officials and combined forces of the MILF and the Moro National Liberation Front.
Reports reaching the Intelligence Service of the Armed Forces of the Philippines at Camp Aguinaldo yesterday noon, said armed supporters of Datu Piang, Maguindanao Vice Mayor Genuine Kamaong, provincial board members Datu Wala Adzis and Tamano Mamamalapat were still battling the group of MNLF Commander Mando Tambungan and Ebrahim Makamapan (alias Commander Talyo) of the MILF at Barangay Bangket, Datu Saudi Ampatuan. — Jaime Laude, AFP