He said the squad would not have attacked the suspected fighters if they had not opened fire first.
"I don't want to speculate whether they were members of Jemaah Islamiyah.
"But they are part of a dangerous, armed group that has caused unrest among the people,'' he said.
Police have been hunting for people on a wanted list of 29 suspected of involvement in a series of attacks in Poso district.
Ten have already surrendered, been arrested or killed. Isno Adi Winoto, a spokesman for the national police, said the police would continue to hunt down the suspects and their supporters.
Jemaah Islamiyah has been blamed for at least four attacks in recent years, the most deadly being the 2002 suicide bombings on Bali island that killed 202 people, many of them foreign tourists.
The government has since arrested hundreds of suspects and several others have been killed, including a man shot by Poso police on January 11 said to be a senior Jemaah Islamiyah member.