The leader of Al Qaeda's South Asian branch was killed in a US-Afghan joint raid in southern Afghanistan last month, Afghan officials confirmed on Tuesday.

Asim Umar, who led Al Qaeda in the Indian Subcontinent (AQIS) from its inception in 2014, was killed during a September 23 raid on a Taliban compound in the Musa Qala district of Helmand province.

He “was #killed along with six other AQIS members”, Afghanistan's National Directorate of Security said on Twitter, adding that Umar had been “embedded” with the Taliban.

The raid was part of a lengthy and confusing overnight operation on September 22-23 for which the US provided air support.

Authorities said they would investigate reports that 40 civilians, including children, were killed in an airstrike during the operation.

The NDS said that among the six other AQIS members killed in the raid was a man identified as “Raihan”, a courier for Al Qaeda leader Ayman al-Zawahiri.

US Forces-Afghanistan declined to comment.

Under a stalled withdrawal plan negotiated between the US and the Taliban, Washington agreed to pull troops from Afghanistan if the insurgents abide by security guarantees and cut all ties with Al Qaeda.

The US and the Taliban had been negotiating for a year to reach a deal that would have cut US forces in Afghanistan and could have paved the way to a reduction in violence, but President Donald Trump scuttled that agreement last month, citing Taliban violence.

Even if the deal had been finalised, observers doubted whether the Taliban would ever really separate from Al Qaeda.

The US invaded Afghanistan after the Taliban refused to hand over Al Qaeda's leader Osama bin Laden following the September 11, 2001 attacks against America.

The middle-aged Umar was relatively unknown when he was picked to lead the newly created AQIS in 2014. The jihadist branch was established to try to rouse fighters in India, Bangladesh and Myanmar.

Umar — an alias — was named by al-Zawahiri in a video message.