"He left his base and drove to his home district to join Hezb-i-Islami," Kunar governor Shuja-Ul Mulk Jalala told AFP, referring to an insurgent group that fights alongside Taliban militants.
Museeb Khan was an officer in a special force unit assigned to conduct complex operations against the Islamist rebels who wage a guerrilla war against US-led NATO forces and the Kabul government.
The defection will be a blow to the development of the country's special forces as they increasingly take on high-target missions from elite US soldiers ahead of the NATO coalition's withdrawal by the end of next year.
Jalala said a manhunt had been launched to find Khan, who also escaped with some unidentified military equipment.
Zubair Sediqi, a purported Hezb-i-Islami spokesman, told AFP that the officer had been in contact with the group before his defection. He gave no further details.