Identification efforts were under way at the national police hospital in Jakarta on the body of the man flown Saturday afternoon from Temanggung district, state-run Antara news agency reported.
National police chief General Bambang Hendarso Danuri told a press conference that he was still unable to confirm whether the man killed was indeed Noordin until DNA tests were completed.
Danuri said police would compare the DNA with samples taken from Noordin's family in Malaysia.
Elite Detachment 88 anti-terror police besieged a house in a remote village in Central Java district of Temanggung for 18 hours. Local media reported the lone man had yelled to police that he was Noordin.
The siege followed the arrests of two men at a marketplace in Temanggung who are believed to have told police Top was at their uncle's house.
Live television footage of the raid showed explosive-detection robots equipped with cameras entering the house and several explosions were heard. The suspect was found dead in bathroom.