JAKARTA, Indonesia -- The head of Southeast Asia's most feared terrorist group was arrested along with his military chief, police said Friday, claiming a breakthrough in the fight against extremists in the world's most populous Muslim nation.

Authorities warned, however, that Jemaah Islamiyah -- blamed for the 2002 Bali bombings and other attacks -- and breakaway factions could still carry out strikes against Western and Christian interests.

Zarkasih, identified for the first time as the group's overall leader, was captured June 9 on Indonesia's main island of Java, hours after anti-terror police closed in on militant chief Abu Dujana, said Brig. Gen. Suryadarma Salim.

Police initially said Wednesday that Dujana was Jemaah Islamiyah's main leader. However, following two days of intensive interrogation, they said Zarkasih held that post.

Like other top Jemaah Islamiyah members, Zarkasih went by several aliases and underwent military training in Afghanistan in the late 1980s, where he learned bomb-making and arms handling.

"I became the emergency head ... in 2005," Zarkasih, 45, said in a videotape shown to reporters, adding that the selection came amid a police crackdown that has crippled the organization in recent years.

In another videotape, Dujana described himself as "head of the military wing" of Jemaah Islamiyah since 2005.

Jemaah Islamiyah wants to create an Islamic state -- violently if necessary -- across much of Southeast Asia. Its members have long been involved in attacks on minority Christians in eastern Indonesia and fueled an insurgency in the southern Philippines.

A splinter group headed by Malaysian fugitive Noordin Top has been blamed for the 2002 bombings on Indonesia's resort island of Bali; the 2003 and 2004 attacks on the J.W. Marriott Hotel and the Australian Embassy in Jakarta; and the 2005 triple suicide bombings on restaurants in Bali.

The suicide bombings -- some of which police say were carried out with funds and direction from al-Qaida -- together killed more than 240 people, mostly Western tourists.

Sidney Jones, a leading expert on Jemaah Islamiyah, said while Zarkasih and Dujana likely promoted religious unrest on Sulewesi island in recent years, she did not think they played an active role in the bombing campaign.

But she described the arrests as "hugely significant."

"I think it's going to throw the organization in a state of confusion for awhile," she said.

Police said Dujana and Zarkasih would be charged with violating anti-terrorism laws in relation to a haul of firearms and explosives seized in central Java earlier this year.

Aided by U.S. and Australian funds and expertise, anti-terrorism police have arrested about 300 militants in recent years, of which 200 have been convicted. Five received death sentences and many others have been given lengthy prison terms.

Among those previously arrested were Abu Rusdan and Abu Bakar Bashir, both of whom police and former militants have said led Jemaah Islamiyah in the early 2000s.

Bashir was found guilty of giving his blessing to the 2002 Bali attacks, but his conviction was overturned after he spent more than three years in jail. Rusdan served 21/2 years for sheltering a known terrorist.

Both are free and have returned to preaching an uncompromising brand of Islam.

Top, who is considered the country's most dangerous militant, remains at large. He is accused of playing a direct role in all of the major suicide bombings in Indonesia in the last five years.

Salim said Top had never been a member of Jemaah Islamiyah, and that Dujana and Zarkasih did not agree with his tactics. Despite their differences, he said they "protected each other."

Indonesia's top detective, Lt. Gen. Bambang Hendarso Danuri, said the hunt for other terrorist suspects was continuing on Java and Sulawesi islands, where the network was trying to rebuild.

"Jemaah Islamiyah hasn't been destroyed," he said, amid claims that they continue to collect guns, ammunition and explosives. "They are still recruiting people and holding military training" in the southern Philippines.

Indonesia has not made it a crime to belong to the group, which was formed in Malaysia in the late 1990s.