An alleged leader of the Jemaah Islamiah militant group said bombings in Indonesia had hurt Islam's cause there, but warned of more attacks by small terrorist groups working independently and influenced by internet teachings.

In an interview with the Associated Press on Friday, Abu Rusdan said the terrorist campaign had divided the militant movement in the world's most populous Muslim nation, and pointed to a possible opening for authorities trying to further isolate extremists.

Rusdan is an Afghan-trained militant believed by police and the United States to be a key leader in JI, the shadowy South-East Asian network that spawned many of the region's terrorists and is believed to have received funds and direction from al-Qaeda.

In the interview in his large family house in Kudus, a town on Indonesia's main island of Java, Rusdan declined to condemn the militants responsible for the 2002 Bali nightclub bombings and other attacks, saying only that their actions "were counterproductive".

More than 200 people died in the Bali bombings, including 88 Australians.

"We cannot call what they did an act of evil, let alone terrorism," he said. "But we must see the objective facts: Those actions did not bring positive results in efforts to spread the faith in Indonesia. We need to tell them to think again."

The Bali bombings thrust the mostly moderate, secular country onto the front lines of the war on terrorism. Three other suicide attacks on Western targets in the country have since killed more than 40 other people.

Rusdan, 46, said he had no role in terrorist activities, but he danced around questions over his involvement in JI.

Police and analysts say he took over as head of the group's "mainstream" faction in 2002 – after the arrest of former leader Abu Bakar Bashir – but likely had no direct knowledge of the bombings carried out.

Rusdan was arrested in 2003 and sentenced to three-and-a-half years in jail for hiding one of the militants convicted in the Bali blasts, but he was released in late 2005. Indonesia has not made membership of JI a criminal offence.

Rusdan said more attacks, carried out by independent groups, were likely. "No one can control groups who want to do those kinds of actions," he said.

"Many people are not satisfied about the conditions in Indonesia. They can do many things under the influence of teachings on the internet or books that are circulating widely."

Rusdan left for Afghanistan in 1985, but he declined to talk about his activities there. He then lived in Malaysia, where he was close to some of South-East Asia's most notorious terrorists, including Hambali, who is now in US custody.

In 2005, the US government listed Rusdan as a terrorist leader and ordered banks to block any financial assets he may have there.