Prosecuting authorities will be formally merged in October
Prosecutors and military police are to forge closer links as part of a reformed courts martial system.
Bruce Houlder, QC, the first civilian to head the Service Prosecuting Authority, told The Times the aim was to create more "robust" practices.
The authority replaces separate prosecuting boards for the Army, Royal Navy and Royal Air Force.
The reforms come after six soldiers were cleared over the death of Iraqi hotel receptionist Baha Mousa in 2003.
The three separate prosecuting authorities will be formally merged in October.
Mr Houlder said the proportion of courts martial convictions was slightly higher than in civilian cases.
But he said the collapse of high-profile cases had given an "unfair impression" that prosecutors had not performed as well as they might.
He told the Times there was a significant difference between personnel deliberately flouting the law and "young soldiers acting to the best of their ability who make a terrible mistake".
He added that he had written to all commanding officers to reassure them he acknowledged the special requirements of an armed forces justice system.
In the Baha Mousa case, Cpl Donald Payne was jailed for a year in 2007 after pleading guilty at a court martial to inhumanely treating civilian detainees in Basra in 2003.
Six other soldiers were cleared of the alleged abuse of the detainees, who included Mr Mousa.
A public inquiry into Mr Mousa's death is due to start in the spring.
Attorney General Baroness Scotland has agreed evidence personnel give to the inquiry will not be used against them in criminal proceedings, including courts martial.