Dulmatin has a $10m US bounty on his head
A key Indonesian militant wanted for the 2002 Bali bombings was hurt in a gun battle in the Philippines last week, the Philippines military says.
Dulmatin, believed to have built the Bali bombs, was caught up in fighting on the southern island of Jolo, Lt Almerante Mijares said.
Abu Sulaiman, a leader of the militant group Abu Sayyaf, was killed in the same clashes.
Dulmatin has long been thought to be in hiding with Abu Sayyaf.
"Based on (radio) signal intercepts and human intelligence, Dulmatin and his comrades were wounded," Lt Mijares said.
Lt Mijares said he led the raid on the Abu Sayyaf camp near the town of Patikul on 16 January, which triggered a fierce gun battle between troops and up to 60 Abu Sayyaf fighters.
Top Abu Sayyaf commander Abu Sulaiman, also known as Jainal Antal Sali, was killed in the fighting.
He had a $5m bounty placed on his head by the US, in part for the 2001 abduction of a group of tourists on the island of Palawan, which led to the deaths of two Americans and several others.
Days after the January attack, tests on a body found in a remote part of Jolo confirmed it was that of the former head of Abu Sayyaf, Khaddafy Janjalani.
He is believed to have been killed in clashes with troops in September 2006.
Dulmatin has long been on Indonesia's most wanted list, and the US has also offered a $10m reward for information leading to his death or arrest.
An Indonesian national, he is believed to be one of the few JI militants able to assemble and explode large chlorate and nitrate bombs.
Abu Sayyaf - the smallest and most radical of the Islamic separatist groups in the southern Philippines - is believed to be providing protection for JI members in return for bomb-making expertise and training.
US troops and military advisers have been in the southern Philippines for the past four months to provide training and intelligence for an offensive on militants hiding in Jolo.