The police shooting in central Java was initially hailed as a triumph. The operation came less than a month after deadly Jakarta hotel bombings that Noordin was believed to have ordered. He has evaded the authorities while carrying out a series of high profile attacks since at least 2003.
But police have now conceded doubts about the identity of the dead men appear credible. One policeman said: "It's not him.
We know from his facial structure as well as his fingerprints. We're continuing to track his whereabouts."
According to the police spokesman, Nanan Soekarna: "Whoever the man is, it should be proved in a scientific way." DNA test results could take two weeks.
The bullet riddled body of the dead man was photographed by the media as it was removed from the scene of the 17 hour siege on Saturday.
According to Sidney Jones, a regional security expert with the International Crisis Group: "The picture of the guy doesn't bear any resemblance [to Noordin Top]."
"It's a huge disappointment, the police were convinced they had Noordin in that house," Ms Jones said.
According to the police, they received intelligence that Noordin Top was in the building and during the siege a man inside shouted "Yes, I'm Noordin Top".
Ms Jones said that the escape means Noordin's "legend grows".
Meanwhile, the Indonesian authorities have made several successful raids against his network since the hotel bombings on July 17, when 9 people including 2 bombers died.
Noordin is sometimes linked to the 2002 Bali bombing, which killed 202 people, but many experts believe his prime responsibility is for attacks on Bali in 2005 and on hotels and the Australian embassy in Jakarta since 2003.