MELBOURNE - Fingerprint analysis has confirmed that one of two men reported killed in a central Java shoot-out with police was not Indonesia's most wanted terrorist, Noordin Mohammed Top.

Malaysian-born Top is a prime suspect in last month's near simultaneous suicide attacks on Jakarta's JW Marriott and Ritz-Carlton hotels that killed nine people and wounded 53.

Police hunting for the mastermind of last month's attacks on hotels raided two houses on Saturday, killed two suspected militants, arrested five others and seized explosives and a car bomb, a senior officer said.

Officials were publicly sticking to their line that only DNA tests would confirm the identity of the body, but a source involved in the investigation said Noordin remained at large.

"It's not him. We know from his facial structure as well as his fingerprints. We're continuing to track his whereabouts," News.com.au quoted the police source, as saying.

Noordin was reported by the local media as having been shot dead by police at the end of a 17-hour siege of a remote farmhouse in Central Java.

Senior counter-terrorism official Ansyad Mbai refused to comment on the identity of the body retrieved from the farmhouse, saying DNA tests would confirm whether it was Noordin or not.

Noordin, 40, is is wanted for multiple suicide bombings against Western targets in Indonesia since 2003 which have killed around 50 people and injured hundreds.

He is one of the most wanted alleged terror masterminds in Asia, and has a 119,960 dollars bounty on his head from the Indonesian Government.

A police source indicated that Noordin may have escaped from the farmhouse before police laid siege to it on Friday evening.

Police have come close to arresting Noordin, who leads a breakaway faction of the Jemaah Islamiah regional terror network, several times and have captured or killed some of his closest associates. (ANI)