Stone's report, which has not been made public, recommends separating
fighters from more moderate detainees, the newspaper said.
It also stated that the US is to help build and finance a new Afghan-run prison for suspected Taliban fighters currently held in the Afghan corrections system.
The remaining inmates would be taught vocational skills and moderate interpretation of Islam with the aim of reintegrating them into society.
The review also calls for the training of new Afghan prison guards, prosecutors and judges, the paper said.
The news of the US military review comes against a backdrop of rising civilian and military death toll.
In the latest attack, at least 11 civilians were killed and two others wounded when their vehicle struck a roadside bomb in southwestern Afghanistan, a local government official said on Monday.
Elsewhere, in the country's south, a tornado fighter jet crashed inside Nato's largest base during take-off, injuring the two-member crew.
The crew ejected and were being treated at the Kandahar airfield base hospital, a military spokesman said.
A Russian-owned civilian Mi-8 helicopter crashed at the same base on Sunday, killing 16 people on board.