It was unclear whether the shooting was related to a campaign launched Tuesday against extremist groups in the district of Abeen.
Ahmed Ali Saleh heads the country's special anti-terrorism forces.
Well-informed sources in Amman told UPI Saleh was admitted to Al-Hussein Medical City in Amman. The sources said security was tight.
UPI learned Saleh, a colonel and commander of the Yemeni Special Forces to Combat Terrorism, was shot by a military commander, identified as Ali al-Marani, in the Suwad Haziz camp, 30 kilometers (19 miles) south of Sanaa.
Al-Marani was reportedly killed in an exchange of fire.