Ally of Al Qaeda Killed in Afghanistan Raid, Officials Say, but Taliban Deny It

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.

The presence of the commander of a Qaeda-linked group in a Taliban-controlled district in Afghanistan’s violent south underscored the ties between the Taliban and associates of the militants who carried out the Sept. 11 attacks 18 years ago.

It also cast doubt on the Taliban’s pledge, during recent peace negotiations with the United States, to prevent Afghanistan from reverting to a safe haven for violent extremists.

In its statement denying that a Qaeda leader had been killed in the raid, the Taliban said the “truth of the matter remains that the said operation in Musa Kala district only caused heavy civilian losses.”

Little is known about Mr. Umar. Pakistani counterterrorism officials say he masterminded a plan to hijack a Pakistani navy frigate in Karachi in 2014. Ten paramilitary members were killed, and 15 were wounded.

Pakistani officials said the death of Mr. Umar was a major blow to Al Qaeda in the Indian Subcontinent. He not only recruited a significant number of trained militants, but also compelled a number of local militants to pledge allegiance to his affiliate, the officials said.

“Because of his previous affiliation with various local militant outfits operating in the region, he managed to influence networks of Afghan and Pakistani Taliban, Jihadi groups operating in Kashmir and smaller groups operating in other South Asian countries,” said Raja Umar Khattab, a Karachi-based counterterrorism police official.

A senior Afghan security official said Mr. Umar had managed to build a network of about 1,500 militants across the region, with recruits drawn from South Asia, Iran and Central Asia. Mr. Umar had close ties to the Taliban’s leadership council in Quetta, Pakistan, and his militants provided training to Taliban in Afghanistan and were involved in fighting in the Afghan provinces of Helmand and Nimroz.

Col. Sonny Leggett, a spokesman for the American-led military mission in Afghanistan, confirmed the deaths of the Qaeda members and that “several foreigners associated with Al Qaeda were detained, including multiple persons from Pakistan and one from Bangladesh.”

After the raid, details from the scene were murky; accounts from Taliban-controlled areas are sometimes contradictory. Military officials in Washington said that some civilians had most likely been killed. Government officials in Helmand Province said up to 40 civilians might have died, including members of a wedding party.

A statement from the American-led mission said that the raid was under investigation.

“Because of heavy fighting, we did conduct targeted precision strikes against barricaded terrorists firing on Afghan and U.S. forces,” the statement said. “We assess the majority of those killed in the fighting died from Al Qaeda weapons or in the explosion of the terrorists’ explosives caches or suicide vests.”

Violence has surged in Afghanistan since months of peace negotiations between the United States and the Taliban collapsed last month and Afghan voters went to the polls at the end of September for the country’s presidential election.