Asim Umar, the head of al-Qaeda in the Indian Subcontinent (AQIS), died in a raid on a Taliban compound in Helmand province on 23 September, the National Directorate of Security (NDS) said.
At least 40 civilians were reported to have been killed in the same operation.
The US and al-Qaeda have not confirmed Umar's death.
In a statement shared on Twitter on Tuesday, the NDS said the joint US-Afghan raid took place at a compound in the "Taliban stronghold of Musa Qala" district, where Umar and other AQIS members "had been embedded".
It said six other AQIS members were also killed, "most" of whom were Pakistani. Abu Raihan, said to be Umar's "courier" to al-Qaeda leader Ayman al-Zawahiri, was named as one of those killed.
The NDS shared pictures purportedly showing Umar both alive and dead alongside the statement.
Further details of the operation and what happened to the bodies were not immediately clear.
The presence of a senior al-Qaeda leader in a Taliban compound raises questions about the militant group's willingness to cut ties with jihadists as part of peace talks with the United States.