Dr Mapp said some ended up in the facility known as 17/40 in Kabul, which is one of a number of centres where torture has been alleged, although the UN is still investigating.
He said the CRU have captured 58 suspects with the help of the SAS since their rotation started in September 2009.
"I've been advised by the Defence Force that they have no reports of anyone who's been arrested by the CRU having been tortured."
But the Defence Force did not track each person to ensure that was the case. "Anyone arrested by the CRU, their names are supplied to Nato/ISAF (International Security Assistance Force). We then essentially leave it to Nato/ISAF to do further tracking."
The UN named several facilities where systemic torture took place. Detainees were punched and kicked, beaten with rubber hoses and metal pipes, and threatened with sexual abuse.
From one detainee: "I was tied up from both wrists to the bars of an iron door in the middle of the hallway from morning until lunch time. They put a hood on my head and hung me by my wrists.
"The next day ... they took off my clothes and one of them twisted [my penis] severely until I passed out. After I woke up, I had to confess because I could not stand the pain."
Journalist Jon Stephenson, who has reported extensively on the SAS in Afghanistan, said the Government was complicit in war crimes.
"The Government and the Defence Force are either very stupid, or very dishonest, because the evidence has been there for years, and they have continued to let our troops be involved in transferring detainees to the NDS."
GRIM READING
* UN report shows widespread torture of prisoners held by the Afghan National Directorate of Security.
* The SAS partner the Crisis Response Unit, who arrest suspects and hand them to the Afghan authorities, including the NDS.
* Defence Minister Wayne Mapp has "no information" that people arrested by the CRU have been tortured.