A police spokesman, Ketut Yoga Ana, declined to confirm that Noordin had died or say how many militants were killed in the siege.
'Let's hope so,' Ketut said when asked if Noordin was killed.
Local media said it appeared that the man thought to be Noordin was the only fatality in the raid. Ketut said there were no casualties among the police.
In a separate, dramatic anti-terror raid outside Jakarta Saturday morning, anti-terror police killed two suspected militants, national police chief General Bambang Hendarso Danuri told reporters.
Police seized a 100-kg bomb and explosive materials intended for car bombs from a house, believed to be an earlier safe house for Noordin, Danuri said.
'It's for a very special target,' Danuri said.
Noordin, believed to be the leader of a splinter group of the radical Islamic network Jemaah Islamiah, is also accused of masterminding the 2003 suicide bombing on the same Marriott hotel, which killed 12 people, and the 2004 attack on the Australian embassy, in which 11 people were killed.
Police have come close to arresting Noordin several times in the past and have captured or killed some of his closest associates.