Commander was a rank used by the service organisations of many civilisations.
Maxil was a Commander of the Chancellery Guard. (TV: Arc of Infinity) He was promoted to castellan following Andred's supposed death, (AUDIO: Lies) but later demoted to commander once more after siding with Pandora and Darkel in the civil war. (AUDIO: Appropriation)
When several incarnations of the Doctor were sent to the Death Zone, a Commander of the Chancellery Guard carried out a search of the quarters of Jerricho on the orders of Lord President Borusa and discovered the Black Scrolls of Rassilon. He later shot Jerricho dead as he tried to escape. (TV: The Five Doctors)
The Sontaran Empire had various Commanders of its Divisions, Fleets and Squads.