The hardline Indonesian terrorist group founded by slain militant Noordin Mohammed Top has been left in complete turmoil by the killing of its new leader, analysts say.

Militant brothers Saifuddin Jaelani and Mohamed Syahrir were killed in a shootout with officers from Indonesia's elite Detachment 88 anti-terror squad during the raid on a boarding house on Jakarta's outskirts last week.

Jaelani, also known as Saifuddin Zuhri bin Jaelani Irsyad, was a senior acolyte of Noordin – who was himself killed in a police raid last month – and a key organiser of July's attacks on two Jakarta hotels.

Indonesian police believed Jaelani, little-known before the hotel bombings, had become the new leader of Noordin's Jemaah Islamiah splinter cell.

US intelligence firm Stratfor says Jaelani's death was another damaging blow for the group, which sometimes calls itself Tanzim Qaedat al-Jihad.

"Tanzim Qaedat al-Jihad currently appears to be leaderless, in turmoil and lacking support from the general Indonesian Muslim population," Stratfor says.

"In militant groups, this combination usually breeds factionalism, infighting, and general ineffectiveness in carrying out coordinated, large-scale attacks."

Police believe Jaelani recruited the two suicide bombers who blew themselves up inside the JW Marriott and Ritz-Carlton hotels on July 17, killing seven people, including three Australians.

It was Jaelani, a Yemeni-trained preacher with suspected links to Middle East terror groups, who could be heard calling for the destruction of Australia, the US and Indonesia in video footage released by police earlier this month.

Syahrir, the elder of the two, also helped organise the hotel attacks and construct the bombs used. He once worked as a technician for Indonesia's national airline, Garuda.

Police say they have now caught or killed almost everyone involved in the July 17 attacks.