Local media said the suspect was believed to be Dulmatin, a possible mastermind behind the bombings of Bali nightclubs that killed 202 people.
Dulmatin, an electronics specialist with training from al-Qaeda camps in Afghanistan, was thought to have fled to the Philippines. Like many Indonesians, he uses one name.
However, Aritonang said authorities were still trying to determine the identity of the suspect.
"We will announce who he is as soon as police identify him," Aritonang said.
Police later shot and killed two suspects as they fled on a house where two others were arrested, Aritonang said. One of those killed had been firing a handgun.
Aritonang said another terror suspect had been arrested in Jakarta on Tuesday before the two raids, bringing to 24 the number of suspects taken into custody in Java and Aceh since February 22 in a police crackdown on a suspected Jemaah Islamiyah (JI) cell in Aceh.
Aritonang said the raids on Tuesday were based on information gleaned from those already arrested.