The US says they are Taliban fighters who will probably return to the battlefield to kill coalition and Afghan forces.
Their release was ordered by President Hamid Karzai several weeks ago after his government took over the prison from US troops.
The decision prompted angry condemnation from Washington and strained relations between the two countries ahead of the year-end withdrawal of most international combat troops.
US forces in Afghanistan say some of the men are responsible for killing or wounding dozens of international and Afghan soldiers.
The prisoners were freed from Parwan jail near Bagram airfield, about 28 miles north of Kabul. Prison spokesman Major Nimatullah Khaki said they boarded a bus laughing and smiling.
The US has argued for the detainees to face trial in Afghan courts - citing strong evidence against them, from DNA linking them to roadside bombs to explosive residue on their clothing - but Kabul says there is insufficient proof to hold them.
Mr Karzai has referred to the Parwan prison as a "Taliban-producing factory" where innocent Afghans are tortured into hating their country.
The US military condemned the release which it said would include detainees directly linked to attacks that have killed or wounded 32 US or coalition personnel and 23 Afghan security staff or civilians.
Afghan Defence Ministry spokesman Mohammad Zair Azimi would not comment on US concerns. He said: "Our responsibility is the protection of the prisoners. That is all."
Among those who walked free was Mohammad Wali who the US military says is a suspected Taliban explosives expert who allegedly placed roadside bombs targeting Afghan and international forces.
The military said Wali had been biometrically linked to two roadside explosions and had a fingerprint match on another improvised explosive device.