The chief minister of Baluchistan province, Jam Mohammed Yousaf, issued the order for the prisoners to be freed in time for the Muslim holiday of Eid al-Fitr, which marks the end of the month of Ramadan.
A leader from the minister's party, Maulana Abdul Wasih, said the released prisoners would include members of Jaish-e-Mohammed, one of Pakistan's most notorious militant groups which has been linked to the Taliban.
The prisoners have been allowed two months with their families except for those charged with involvement in terrorism.
President Musharraf outlawed Jaish-e-Mohammed and four other militant groups in January, a month after the attack on the Indian Parliament which Delhi blamed on Pakistani-supported militants.
From the newsroom of the BBC World Service
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