KABUL — American and Afghan commandos killed the head of an affiliate of Al Qaeda in a southern Afghanistan raid last month, according to a statement released Tuesday by Afghanistan’s intelligence agency.

The Taliban denied the assertion, calling it propaganda by “officials of the stooge Kabul administration.”

The intelligence agency’s statement followed weeks of rumors that the militant, Asim Umar, had been killed in the Sept. 23 raid, which was said to have left dozens of civilians dead.

The raid, in the Musa Qala district of Helmand Province, also killed a Pakistani who had close ties to Mr. Umar, the leader of Al Qaeda in the Indian Subcontinent since 2014, and to Ayman al-Zawahri, the current head of Qaeda’s main branch, the statement said. He was identified only as Raihan.