A series of high-profile criminal convictions could be thrown into doubt next week following a protracted legal battle over the use of a controversial informer with strong links to Melbourne’s underworld and law enforcement.

An investigative agency recently lost a four-year court battle against another government department to suppress information that is expected to raise serious concerns about the integrity of Victoria’s justice system.

Victoria's criminal justice system is set to be shaken Credit:Fairfax Media

At the heart of the controversy is how the investigative agency obtained information from an informer regarding Melbourne’s gangland war, despite the informer having a blatant conflict of interest because of their professional role.

It is understood the registered informer provided intelligence on some of the nation's most notorious criminals for more than five years.