The activist group Focus on the Global South, citing US military writings, doctrines and eyewitness accounts, called for an independent investigation into whether the alleged operations violated the Philippine Constitution.
US Embassy spokesman Matthew Lussenhop disputed the allegation.
"Visiting US troops in the Philippines advise, assist, share information with their Philippine counterparts, but they do not engage in combat and they have no direct role in combat operations. Any combat operations are 100 percent Filipino," he told The Associated Press.
A US Special Forces contingent has been deployed in the south since 2002.
Lussenhop said the number of Special Forces troops average "no more than a few hundred at any one time." — AP