Since 2009 NZSAS has taken one person into detention in Afghanistan - a mid-level Taleban commander.
The operation was at the direction of the ISAF and was not conducted in partnership with the CRU, the report said.
That person had subsequently been transferred to US-Afghanistan Government joint custody.
General Jones said in the August report there had been no evidence, or even suggestions that any member of the CRU had tortured or ordered the torture of any person.
"All evidence at our disposal suggests the CRU have acted appropriately in respect o persons they have arrested."
The CRU was now regarded by the International Security Assistance Force as the leading unit of its kind.
General Jones said that under the mentorship of the CRU by the New Zealand Defence Force, the CRU had been specifically instructed on the requirement to handle detainees humanely.
The NZDF would continue to review information on detention practices.
"If credible indications of ill-treatment by partnered forces are identified, the NZDF will respond."
The Red Cross and Afghanistan Independent Human Rights Commission had been informed of the detention.
General Jones said the Defence Force had an arrangement with the Afghanistan Ministry of Foreign Affairs concerning the transfer of detainees between NZDF and Afghan authorities call the ATD. But he would not release it because it was classified.
"The arrangement is classified and has not been released out of respect for the wishes of the Government of Afghanistan."
Commenting on the UNAMA report on torture, General Jones says the report was accepted by ISAF as "well researched and credible."
It detailed torture and abuse in some facilities run by the National Directorate of Security (NDS), Afghan National Police (ANP) and the Ministry of Justice.
"These findings are of considerable concern.
He said that since becoming aware of the likely content of the UNAMA report in early September "NZDF force in Kabul have ensured that they know were persons who are arrested during CRU operations are taken after arrest."