A Karzai-appointed investigation panel found six Afghan detainees at a British-run facility at Kandahar Air Field in the south and another 17 at a British detention facility at Camp Bastion in Helmand province, according to commission leader Gen. Ghalum Farooq Barakzai.
He said no detainees were found at the American facilities but said they should no longer even exist.
The coalition has in recent years transferred thousands of detainees to Afghan authorities, and earlier this year American and UK officials protested when Karzai ordered dozens of suspects they considered a danger to be freed instead of tried in court.
British military authorities said in a statement that "detainees are held at the request of the Afghan authorities when there is evidence linking them to criminal activities."
The statement said detention is crucial to removing insurgents trying to injure and kill troops and civilians.
The flare-up is the latest rift between Karzai and his ostensible allies, who have been frustrated with the president's increasingly anti-American rhetoric and his refusal to sign a security agreement to keep a small US force of trainers in the country after the NATO-led coalition ends its mission and withdraws at the end of the year.