"As of now, we are conducting DNA test to confirm if it is really his body," he said on Tuesday.
Dulmatin, a member of Jemaah Islamiyah (JI), the al-Qaeda-linked group blamed for a series of bombings across South-East Asia, was accused of masterminding the 2002 Bali nightclub bombings which killed 202 people.
The US state department has offered a $10m reward for information leading to Dulmatin's capture under its "Rewards for Justice" programme.
In 2003, Dulmatin was thought to have fled to the southern Philippines where he was reportedly wounded during a clash with Philippine troops in late January this year.
The gunfight also killed a top leader of the Abu Sayyaf, a group based in the southern Philippines accused of being behind a series of bombings and kidnappings.
Dolorfino said the gunshot wounds in the corpse's head, chest and right foot were consistent with earlier accounts of Dulmatin's injuries in the gunfight.
|A total of 202 people were killed in the Bali |
attacks on October 12, 2002 [GALLO/GETTY]
He said a positive DNA result would be "a big blow" to JI and the Abu Sayyaf.
Philippine intelligence officials say they believe the Abu Sayyaf is providing protection for JI members in return for bomb-making expertise and training.
Major Eugene Batara, the spokesman of military forces in the south, said the body has been taken to Zamboanga and will be given a "decent burial" once enough samples are taken.
DNA tests are expected to take about up to two weeks before any result on the corpse's identity is known.
Philippine forensics experts have requested help from the US FBI to carry out the tests.
Rear Admiral Emilio Marayag, head of naval forces in the region, said experts will compare samples from Dulmatin's body with those taken from his family.
Dulmatin's wife and six children were separately detained in the Philippine province of Mindanao in 2006 before being deported to Indonesia last year.