"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.
'Look' how the Sheena Bora case has taken a toll on Indrani Mukerjea
Photos: Katrina Kaif, Parineeti Chopra, Shilpa Shetty's movie outing in Juhu
Birthday special: 14 Bollywood actors who made it big on TV
Photos: Vaani Kapoor, Poonam Pandey, Sana Khan at fashion event
Photos: Rishi Kapoor, wife Neetu, daughter Riddhima at book launch