The body of Captain Ken Masters, the commander of 61 Section of the Special Investigations Branch (SIB), was found in his bed at the airport at the weekend. The death is being investigated by the SIB.
Defence sources said the death was "not due to hostile action and also not due to natural causes".
However, it is believed that investigators have not found a suicide note, nor firearms related to the incident. Capt Masters was not receiving any medical or psychological treatment.
Friends and colleagues of Captain Masters, who was married with two children, said that his death had come as a "total surprise".
After his body was found early on Saturday evening a siren sounded over Basra camp, flares were fired in the air, and all military personnel were confined to barracks .
Despite being of middle-rank, Captain Masters was in charge of all serious incidents involving the British military in Iraq.
It was not immediately known which particular cases he had been personally involved in investigating. The British military is, however, looking into several dozen cases.
Seven members of the Parachute Regiment are on trial for the murder of an Iraqi teenager, Nadhem Abdullah.
Several Fusiliers have been convicted at a court martial in Osnabrück, Germany, of abusing civilians and photographing the acts.
Some soldiers have been charged in relation to the death of a hotel receptionist, Baha Musa.
A spokesman for the British forces in Basra said: "The commanding officer of 61 Section, Special Investigations Branch, Capt Ken Masters, was found dead last night at a military establishment in Iraq.
"The matter is now under investigation and until this is completed it will be inappropriate for me to make any further comment. It was not due to any hostile action. It was not down to natural causes."
A military source said "This has come as shock to us. Ken was not suffering from depression or anything that indicated that he would take his own life."Reuse content