Wahidullah Khan, the commando, was arrested on suspicion of opening fire and killing a Czech soldier at an Afghan base with a small NATO presence on October 22. He was transferred by Afghan forces into NATO custody shortly after being detained.
Two other Czech soldiers were wounded in the shooting, the fourth insider attack from Afghan forces against NATO partners in 2018.
Khan was handed back over to the Afghans, beaten and unconscious, hours later and died shortly afterwards, anonymous Afghan officials told the New York Times. That paper reported that a photograph of Khan showed "extensive blunt force trauma" to Khan's face and head.
An American official told the paper that a team from the US Army's 7th Special Forces Group helped transfer Khan to the custody of Czech forces. It isn't clear who was responsible for the beating.
A spokesman for the Czech Ministry of Defense said on Monday that they "strongly deny any such accusations" that their forces were involved in Khan's killing.
One member of the local provincial council in Herat said that "from what we know, that soldier died of torture," but wasn't sure whether the Americans or Czechs were responsible.
Khan's father told the paper, "When we washed him, he had no bullet wounds, but his entire body was bruised."
According to the young commando's brother, he'd been in an elite unit for just over a year after he gave up farming when the local Daesh affiliate nearly seized his home district.
A senior Afghan security official in the capital told the Times that the government considers Khan to be a "Taliban infiltrator," the paper reported. His family denied the charge.
"Nobody told us what happened," his brother said. "Nobody has told us who arrested him, who gave him to the foreigners."
Discontent with the lingering American presence is growing in Afghanistan, Sputnik News has reported, with conspiracy theories growing about an intentionally protracted war with ulterior motives being waged by the US.
Khan's attack on NATO forces came within days of an Afghan guard killing a police general beloved by many Afghans and friendly to US forces during a shootout at a palace in Kandahar. US General Austin Miller, the US' senior commander in the country, was nearly shot in the fight.