Ammunition and equipment for making firearms, including a 3D printer, has been seized from the house of senior Mongol Shane Middleton.
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Echo Taskforce detectives arrested Mr Middleton, his fiance Renee Comeadow and another man, all with links to the outlaw motorcycle gang, after raiding homes in Seabrook and Oakleigh South about 6am on Thursday.
The firearms-manufacturing equipment and a small amount of drugs were seized from the house in Mintaro Way, Seabrook.
Mr Middleton, a 26-year-old believed to be the gang's sergeant-at-arms, and Ms Comeadow, 27, were arrested.
Mr Middleton was charged with attempting to pervert the course of justice, possessing cocaine, steroids, ammunition and possessing a prohibited weapon.
Ms Comeadow was charged with attempting to pervert the course of justice and committing an indictable offence whilst on bail.
A stolen motorcycle was seized from a house in Fleming Court, Oakleigh South and a 29-year-old man was arrested.
He was charged with attempting to pervert the course of justice, three counts of theft of motor vehicle and possessing ammunition.
All three are expected to face the Melbourne Magistrates Court later on Thursday.
"The warrant is part of an ongoing Echo Taskforce investigation in relation to perverting the course of justice," a police spokeswoman said.
Mr Middleton was shot in the leg in November, but it is unclear who shot him. He was driven to Sunshine Hospital by Ms Comeadow.