MANILA — An elite American military counterterrorism unit that has been operating in the southern Philippines for more than a decade is being phased out, the Pentagon’s Pacific Command said Thursday.

The Joint Special Operations Task Force Philippines — which was formed after the Sept. 11, 2001, attacks — was established to help train and advise the Philippines in its fight against rebel groups linked to Al Qaeda. The unit was one of dozens worldwide that tried to fight potential terrorist groups, before they could strike the United States.

American Special Forces will continue to help Philippine security forces counter a smaller, lingering Islamist threat, but the size of the mission will drop in the coming months to a dozen or so advisers from its current 320 service members, based in Mindanao in the south, American officials said.

“Our partnership with the Philippine security forces has been successful in drastically reducing the capabilities of domestic and transnational terrorist groups in the Philippines — to the point where they have largely devolved into disorganized groups resorting to criminal undertakings to sustain their activities,” said Capt. Masato Itoh of the Marine Corps, a spokesman for the Pacific Command in Hawaii.