"The body was obviously that of a terrorist, it is just a question of whether or not it was Noordin Top or not.
"Even if it was not Noordin Top it is an achievement on the part of the police to raid that house where they found explosives and militants."
One of Noordin's wives and children were travelling to the capital to provide samples, Dynno Chressbon, another government adviser, said.
Chressbon also expressed secpticism that Noordin had been killed.
"I indeed doubt that the victim is the suspected terrorist Noordin Top," he said, adding that he would never have allowed himself to be left alone at a hideout.
Police moved in on a house near the village of Beji late on Friday where a man resembling Noordin was said to be hiding, and after heavy fighting it was reported that he had been killed.
Sidney Jones, a consultant for the International Crisis Group, said that police had seemed to have been convinced that Noordin was inside the building during the siege.
"That confidence was quite high up until the time they found the body. Then it became increasingly clear it might not be Noordin after all," she told Al Jazeera from Jakarta.
"There was information coming from two people in the area that Noordin had been at the house and acting on that information this huge operation was undertaken.
"There was reason to believe that he was in the house and they have to be incredibly disappointed if it does not prove to be Noordin."
Noordin is accused of planning July's suicide bomb attacks on the Marriott and Ritz-Carlton hotels in Jakarta that killed at least nine people.
He heads an Islamist splinter group with connections to Jemaah Islamiyah, which is fighting for an Islamic state in southeast Asia.
In a video in 2005, Noordin 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 is also wanted in connection with the deaths of more than 220 people in bomb blasts on the resort island of Bali in 2002 and 2005.
Police said on Saturday that a separate raid had foiled a plot by suspected associates of Noordin to attack the president's home outside Jakarta.
"We have optimised and increased security for him and his family," Sagom Tamboen, a military spokesman, said.
"Based on the police information that there is a cell group that wanted to attack RI-1 [Yudhoyono], then we act according to the
Two suspected would-be suicide bombers, who were planning a use a lorry packed with explosives, were shot dead by police at their rented house in Bekasi as they tried to resist arrest, police said.