Dharma tracked Noordin for six years until his intelligence unit was dismantled by the Indonesian government.
Ansyaad Mbai, Indonesia's security ministry's anti-terror desk chief, also blamed Noordin, whose group broke-away from Jemaah Islamiyah after an alleged falling out with the group's leadership over the targeting of civilians.
"There are strong indications that Noordin Top's group is behind the attacks because the bombs were hand-made and the tactic was suicide bombings," Mbai said, adding they have been methods used by Top in the past.
The suicide bombings at the hotels in the Indonesia capital are the fourth attacks allegedly masterminded by Noordin in the country.
He is thought to have been behind the attacks on the Jakarta Marriott in 2003, the Australian embassy in 2004 and on a series of restaurants in Bali in 2005 in which more than 20 people were killed.
Sidney Jones, of the International Crisis Group, told Al Jazeera that one of the prime suspects "has to be Noordin Top".
"The police were actively looking for him just last week in a town in central Java where they found explosives similar to those used in the hotels [attacks]," she said.
"They have been close on the trail of some of these people in the past and I am sure we will see a wave of arrests in the aftermath of this bombing."
The equipment found in the raid last week on an Islamic boarding school in Central Java, carried out as part of the hunt for Noordin, was said by police to be the same as those used in Friday's attack.
The bombs are thought to have been brought fully assembled into the hotels, despite airport-style security measures and were packed with nails, ball-bearings, nuts and bolts to maximise the devastation.
Police said the bombs were "identical" to ones previously used in Jemaah Islamiyah (JI) attacks, but the group has denied involvement in the recent attacks.
Jibril, a long-time member of JI, told Al Jazeera that his organisation was not involved in the attacks.
"JI is an organisation with a very clear goal - we don't fight against an enemy who is not targeting Muslims," he told Al Jazeera.
"Indonesia is not a country attacking Muslims, so we don't commit attacks here."
Investigators are sifting through body parts and other forensic evidence, attempting to identify the bombers involved in the attacks.
Police say there were three suicide bombers involved in the attack, and DNA evidence, including a severed head, are under examination.
The bombers are said to have posed as guests at the hotels, checking in two days before the attacks.
Security video from the hotel shows a man with a suitcase and backpack entering the hotel restaurant shortly before an explosion.
Police have not confirmed whether the man is a suspect.
|Over 50 people, many of them foreigners,
were wounded in the attack [AFP]
Speaking to Al Jazeera, the head of security at the Marriott said: "We had two security officers who saw this man ... carrying a big back pack on [his front].
"[When questioned] he said I'm going to see my boss ... [but] couldn't come up with the name and he just kept walking.
"He moved forward five metres and the bomb detonated."
General Bambang Hendarso Danuri, Indonesia's national police chief, called on hotels and shopping malls across the mainly Muslim archipelago of 234 million people to raise their security protocols in response to the bombings.
The attacks triggered the cancellation of a planned Manchester United friendly against an Indonesian All-Star team scheduled for Monday, a decision that caused great dismay among football fans in Indonesia.