But doubt grew after those who saw the body said it did not resemble Noordin.
The raid followed the arrest of two men believed to be Noordin's accomplices.
In a separate raid on a house near Jakarta Saturday, police said they killed two men believed to be prospective suicide bombers and seized 500 kg of explosives intended to be car bombs.
Citing a confession from one of five suspects arrested before the raids, police said Noordin held a meeting in late April to discuss a plan to assassinate President Susilo Bambang Yudhoyono this month to avenge the execution last year of three militants convicted in the 2002 Bali bombings.
Noordin, believed to be the leader of a splinter group of the radical Islamist terrorist network Jemaah Islamiah, is also accused of masterminding the 2003 suicide bombing on the same Marriott hotel in Jakarta, which killed 12 people, and the 2004 attack on the Australian embassy in the Indonesian capital, in which 11 people were killed.
In a video message, the man believed to be Noordin also claimed responsibility for the triple suicide bombings on restaurants in Bali in 2005.