A cousin of Khan, who was shot dead by police after killing two Cambridge graduates in a knife rampage on November 29, told the news site his parents and other close family members would bury him in their home village of Kashmir.
The convicted terrorist's parents wanted to keep the burial "low key" and didn’t want to bury him in the UK “because they were scared,” the cousin told Sky News.
It is understood a pre-burial ritual known as a Janaza was carried out in a Birmingham mosque before Khan’s body was flown to Islamabad International Airport.
It comes after the terrorist’s UK-based family, who live in Stoke, said they were “saddened and shocked” by his actions which they “totally condemned”.
In a short statement released on Tuesday, via the Metropolitan Police, they said: "We totally condemn his actions and we wish to express our condolences to the families of the victims that have died and wish a speedy recovery to all of the injured.
"We would like to request privacy for our family at this difficult time."
Jack Merritt, 25, and Saskia Jones, 23, were both stabbed to death by the 28-year-old during a prisoner rehabilitation event at Fishmongers' Hall.
Khan, who was living in Stafford, was given permission to travel into the heart of London by police and the Probation Service.
Armed with two knives and wearing a fake suicide vest, he was tackled by members of the public, including ex-offenders from the conference, before he was shot dead by police.
The three injured survivors of the attack have been discharged from hospital and are “recovering well”, medics said today.
The City of London coroner declined the Standard's request for comment on the alleged repatriation of Khan's body.