The decision comes despite rights groups' appeals to Libyan authorities to hand him over to the International Criminal Court in The Hague for trial, amid fears that he may not get a fair trial in Libya.
A trial in the capital, Tripoli, would mark a small step forward, however, for the central government, which has been struggling to unify the country since Moammar Gadhafi's capture and killing last year.
Seif al-Islam had been held until now by his captors, ex-rebels from the town of Zintan, one of dozens of militias across the country operating outside government control. For months, the Zintan militia refused to give him up to Tripoli officials.
Mohammed al-Hareizi, spokesman of the ruling National Transitional Council, said Seif al-Islam will be transferred to Tripoli within 10 days.
"He will be tried for rape, murder, corruption," al-Hareizi told reporters in Tripoli.
Seif al-Islam backed his father in his brutal crackdown on rebels in the regime's final days, warning of "rivers of blood" if demonstrators refused to accept government offers of reform. -- AP