JAKARTA - Indonesia will prosecute a top Islamist militant for his alleged role in the 2002 Bali bombings after Pakistan handed him over, the head of the country's counter-terrorism agency said on Thursday.

Pakistani forces captured Umar Patek, a bomb-maker for militant group Jemaah Islamiah who is wanted by the United States, Indonesia, the Philippines and Australia, in January in Abbottabad, a garrison town in Pakistan, where US Navy SEALS killed al Qaeda leader Osama bin Laden in a secret raid in May.

Patek arrived in Jakarta on Thursday, and was taken to a detention centre, counter-terrorism chief Ansyaad Mbai told Reuters by telephone.

"We will interrogate him... and also we will bring him to court and charge him," Mbai said.

Security analysts say Patek is one of the few Indonesian militants who would be able to explain the connections and extent of cooperation between Islamist militant groups in Asia.

However, security experts fear that his presence in Indonesia's prison could mean he could spread his bombing-making skills to other inmates. Mbai said he could become a "breath of fresh air" for militants, inspiring them to launch more attacks.

The attack on a nightclub in the Indonesian resort island of Bali in 2002, for which Patek allegedly assembled the bombs, killed 202 people.

Since then, several key figures in the Southeast Asian network Jemaah Islamiah (JI) which was blamed for the attacks have been killed, captured or jailed. In June, a court sentenced Abu Bakar Bashir, the spiritual leader behind the Bali bombings, to 15 years in jail.