The ministry named the officer as Captain Ken Masters.
"On Saturday 15 October 2005, the body of Captain Ken Masters was discovered in his accommodation in Waterloo Lines, Basra," the ministry said in a statement.
"He had been responsible for the investigation of all in-theatre serious incidents, plus investigations conducted by the general police duties element of the theatre investigation group."
An inquiry into the circumstances of his death has been opened, the ministry said.
Some 8500 British troops are stationed in Iraq. Deaths from all causes have so far totalled 95.