Top died in a shoot-out with police in Java on Thursday.
National police chief Bambang Hendarso Danuri says Top was one of four people killed during a raid in central Java. He says fingerprints and hair samples from the body match.
A presidential spokesperson says officials are sure they have got their man this time (Top was wrongly pronounced dead earlier this year), with President Susilo Bambang Yudhoyono describing his death as a significant victory.
Top led the Jemaah Islamiah group, which was behind the Bali bombings in 2002 that killed 202 people, including three New Zealanders.
The ABC reports he was also involved in the recent bombings of hotels in Jakarta, in which a New Zealander and eight others were killed.
The police say further evidence of links with Al Qaeda was found inside the house.