He said that Indonesian officials were co-ordinating with Noordin's family in Malaysia to return his body "as soon as possible" for a funeral.
Counterterrorism troops sealed off the area near the house in a suburb of Solo city late on Wednesday, searching for suspects involved in the July 17 attacks on the Ritz-Carlton and JW Marriott hotels in Jakarta which left nine people dead and 53 wounded.
Noordin was believed to have headed a splinter group with connections to Jemaah Islamiyah, a group fighting for an Islamic state in Southeast Asia.
In a 2005 video, he claimed to be al-Qaeda's representative in Southeast Asia and to be carrying out attacks on Western civilians to avenge Muslim deaths in Afghanistan.
He was also wanted in connection with the Bali bombings in 2002, which killed more than 200 people, and a number of other deadly attacks.
Susilo Bambang Yudhoyono, the Indonesia president, said that the death of Top "could reduce the seriousness of terrorist threat to Indonesia".
But he cautioned that "it doesn't mean that the cells and organisations that work and move in Indonesia and in Southeast Asia have been crippled".
John Harrison, an expert on terrorism at the Institute of Defence and Strategic Studies in Singapore, told Al Jazeera that it may difficult to replace Noordin because "there are very few individuals that combine the charisma, the organisational abilities plus the connections that he had".
But he cautioned that Jemaah Islamiyah (JI), the group Noordin was linked to, is "always able to replace individuals".