The vicious brawl between men linked to the Bandidos and Comanchero gangs broke out at 9.15am on Tuesday in the prison's gymnasium.

A prison source said the fight lasted more than two minutes, and left two men with non-life-threatening stab wounds.

Two guards are understood to have been overcome by capsicum spray, which was used to bring the skirmish under control.

A Victoria Police spokesman confirmed that two men had been taken to hospital with minor injuries during an altercation that involved up to seven inmates.

The incident is the subject of an investigation by police and Corrections Victoria. The probe is expected to focus on why rival gang members had not been segregated to avoid an outbreak of violence.

While the Comanchero gang has been embroiled in a long-running feud with the Rebels bikie gang, it is not known if tensions have recently been inflamed with the Bandidos.

The two gangs have a history of enmity dating back to the Milperra massacre in 1984, when six gang members and a 14-year-old bystander were killed and 28 people injured during a wild shoot-out south-west of Sydney. The rivalry was originally sparked when a group of Comancheros tried to break away from the gang to form the first Australian chapter of the Bandidos.

Port Phillip Prison in Truganina houses some of Victoria's most dangerous criminals, many of whom are usually segregated on the basis of gang affiliations.

In 2015, the maximum security facility was placed on extended lockdown after the discovery of plans for a violent uprising.

An intelligence unit at the prison found that inmates were plotting to seize control of the facility by staging a fight and then overpowering guards.

Corrections Victoria and private security company G4S, which operates Port Phillip Prison, responded to the threat by relocating several violent inmates to other prisons and increasing the number of guards.