(Reuters) - The U.S. Federal Bureau of Investigation said on Wednesday it has confirmed that Zulkifli bin Hir, one of its "most wanted terrorists," was killed in a raid in the Philippines in January.

The U.S. State Department had offered $5 million for the arrest of bin Hir, a Malaysian member of the al Qaeda-linked Jemaah Islamiah militant group behind numerous bombing attacks in the Philippines.

Investigators said they had a difficult time confirming bin Hir's death because he was killed in a gruesome raid that went awry and left 44 police commandos dead.

Previously, the FBI reported that it had identified body matter at the scene that it believed belonged to bin Hir because of a DNA link between the matter and one of his siblings.

Three years ago, the Philippine military reported bin Hir died in an air strike, but he surfaced again last year in Mindanao under protection of a Moro Islamic Liberation Front splinter group.

In a statement, David Bowdich, assistant director in charge at the FBI Los Angeles Field office said the agency has now taken bin Hir off its Most Wanted Terrorist list and thanked the Philippine police.

"Once again, the men and women of the FBI express sincere condolences to the brave officers of the Special Action Force who lost their lives while attempting to apprehend this dangerous fugitive," Bowdich said.