While Noordin has not been officially named as being behind the Jakarta bombings, officials and analysts have made clear he is the chief suspect.
Vaessen said: "It's still not confirmed that he was actually connected to the latest bombings at the Marriot and Ritz-Carlton Hotel but ... according to terror experts, there's only one man in Indonesia who's capable of doing it.
"They say his fingerprints are all over the attacks."
Local media in Indonesia repoted that police were involved in shooting with suspected figthers in Temanggung in Central Java.
Noordin was a key member of Jemaah Islamiyah (JI), an al-Qaeda-linked group that wants to establish an Islamic state across Southeast Asia.
But his group broke away from JI after an alleged falling-out with the leadership over the targeting of civilians.
JI is blamed, among other attacks, for the 2002 Bali nightclub bombing that killed 202 people.
Noordin is thought to have been behind attacks on the Jakarta Marriott in 2003 and the Australian embassy in 2004, and also on a series of restaurants in Bali in 2005 in which more than 20 people were killed.