Red Cross workers are clearing away the bodies
The surviving Taleban shot and wounded two local health officials who had entered a basement on the site to collect corpses. They appear to be still at large, and a third health worker has been reported missing.
The United Nations has added its voice to calls for an enquiry into the deaths of several hundred prisoners during the revolt.
The Northern Alliance commander, General Abdul Rashid Dostum, whose headquarters is at the fort, had warned visiting journalists that two Taleban fighters were still at large.
And the International Committee of the Red Cross said there was isolated resistance below ground in the bunker system inside the sprawling Qala-e-Jhangi fort, where the prisoners had been held after the fall of Kunduz.
The BBC's Catherine Davis, reporting from Mazar-e-Sharif, says the fact that some Taleban appear to have survived, hiding among the dead, has astonished many here.
The fort was not only the scene of three days of fierce fighting, but was also subjected to heavy aerial bombardment.
The fighting ended on Wednesday, and the first journalists to enter the premises described a scene of carnage, with dead bodies littering the ground.
UN High Commissioner for Human Rights, Mary Robinson, has called for an enquiry into events at the prison.
Jose Diaz, a spokesman for the High Commissioner, told BBC News Online that, although the situation had been complex, "there are a lot of unanswered questions."
Mr Diaz referred specifically to reports that in one part of the fort, bodies of prisoners had their hands tied behind their backs.
General Dostum has denied that Taleban prisoners were tied up.
The UK Government, for its part, ruled out any international enquiry into events at the fort.
Clear up
The ICRC has removed about 150 bodies so far.
Simon Brooks, head of the ICRC operation in northern Afghanistan, said they were not sure what the final death toll would be.
He said the priority was to process the bodies as quickly as possible.
The three-day prison revolt was eventually crushed by Northern Alliance forces, backed by US and British special forces.
Most of the Taleban prisoners are reported to have been foreign fighters - Arabs, Pakistanis and Chechens - who were taken to the fort after surrendering in the northern Afghan city of Kunduz.
Local Afghan Taleban were allowed to go free after they surrendered.
It is not clear how the uprising started.
The Northern Alliance said the prisoners launched an attack when an alliance general went to reassure them that they would be well treated.
Other reports said the fighting started when US secret agents began questioning the prisoners to ascertain if any had links to the al-Qaeda organisation.