Gunaratna cited sources within the investigation.
But Indonesian authorities refused to verify whether Noordin was one of those killed.
Bambang Hendarso Danuri, Indonesia's national police chief, said that Indonesia "cannot yet confirm that this is Noordin Top".
Noordin is wanted as a suspect in July's suicide bomb attacks on the Marriott and Ritz-Carlton hotels in Jakarta, as well as in connection with the deaths of more than 220 people in bomb blasts on the resort island of Bali in 2002 and 2005.
Late on Friday police moved in on a house in Central Java where a man resembling Noordin was said to be hiding and a 17-hour siege ensued.
Explosives and heavy gunfire were heard early on Saturday as police moved in on the building.
Witnesses said that at least two body bags were removed from the house shortly after the shooting had ended.
The bodies were reportedly taken to Jakarta where tests were to be carried out to confirm the identity of the dead.
Soon after the bodies were flown to Jakarta, Gunaratna told Al Jazeera: "The DNA has not matched with the body that has been recovered."
Officially, however, the DNA results are not expected until next week.
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 the Malaysian-born head of an Islamist splinter group with connections to Jemaah Islamiyah, a group fighting for an Islamic state in southeast Asia.
Karim Raslan, an Indonesian political commentator, told Al Jazeera that were Noordin to be killed it would be a "very significant coup".
"However, I think that many people will still be concerned as to the extent to which Noordin Top has actually managed to move his group throughout southeast Asia," he said.
In a video in 2005, the Malaysian citizen 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.
Also on Saturday, Indonesian police killed two suspected Islamic fighters and seized up to 500kg of bomb-making material after a raid on a house in Bekasi, near Jakarta, police said.
Bambang Hendarso Danuri, the national police chief, said that the raid was linked to the operation in Central Java and targeted a "cell of NMT," referring to Noordin.
|Police said two other suspects were killed in a raid on a house in Bekasi near Jakarta [AFP]
"We had to shoot them because at the time of the raid they had hand-held bombs that were about to be thrown at the police," he said.
"They were would-be bridegrooms [suicide bombers] with special targets for attacks to be carried out two weeks from now."
Al Jazeera's Step Vaessen, reporting rfom Jakarta, said: "Two bombs have been found, which, according to police sources, were going to be used to bomb the president's house not far from where they were found."
Nanan Soekarna, the national police spokesman, identified the two suicide bombers as a 19 year-old man and 28 year-old man who carried out deadly attacks on the Jakarta hotels last month.
The July 17 attacks on the Marriott and Ritz-Carlton hotels killed nine people and wounded 53 others, including Indonesians and foreigners.
The bombings broke a four-year lull during which there had been no major attacks.