(Recasts with police killing one)

JAKARTA, March 21 (Reuters) - Indonesian police shot dead a militant believed to have links with the leader of Southeast Asian militant network Jemaah Islamiah and arrested several others, a police official said on Wednesday.

One militant was also injured after the suspects opened fire during the Tuesday night raid near the city of Yogyakarta, national police spokesman Sisno Adiwinoto said.

Adiwinoto said the suspects were believed to have links with Abu Dujana, an Indonesian officials say is the current leader of Jemaah Islamiah.

Jemaah Islamiah has been blamed for launching deadly attacks in Indonesia, including the 2002 Bali bombings that killed more than 200 people.

"We have arrested several others to help us hunt for other suspects," Adiwinoto told reporters.

Indonesia, which has seen a string of bombings blamed on Islamic militants in recent years, has already arrested hundreds for involvement in attacks.

The crackdown and differences among members over tactics led to changes in Jemaah Islamiah which saw Abu Dujana emerge as head of the group, according to police.

Muslim cleric Abu Bakar Bashir was arguably the most high-profile figure identified with Jemaah Islamiah. Western and regional intelligence officials say he was its spiritual leader.

But he denied links to the group and last December Indonesia's Supreme Court cleared him of any part in the Bali bombings. The finding came after he had finished a jail term handed by a lower court that said he was part of the conspiracy.

Authorities say several important violent militant leaders remain at large. Countering them is complicated by the operation of individual cells whose members do not necessarily know about the activities of others, and by ideological and tactical splits.

Malaysian national Noordin M. Top, considered a mastermind of the bombing attacks, has been called the most wanted terror suspect in Indonesia.

But establishing his current clout among the militants is difficult, police officials said.

Top, for example, has proclaimed himself leader of a group called the Tanzim Qaedat al-Jihad network, or Organisation for the Basis of Jihad, police say, and its precise relationship to the older Jemaah Islamiah is unclear.

An estimated 85 percent of Indonesians are Muslims. Most are considered moderate, but a militant minority has been increasingly vocal and media-savvy.

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