Police have charged two men with the murder of Melbourne fruiterer Paul Virgona, who was gunned down while driving to work on the EastLink tollway last year.

Key points: A 35-year-old man and 29-year-old man have been charged with murder

A 35-year-old man and 29-year-old man have been charged with murder A 30-year-old man was arrested in relation to drug offences

A 30-year-old man was arrested in relation to drug offences Homes, commercial premises and bikie clubhouses across Melbourne suburbs were raided early this morning

Mr Virgona, 46, was driving to work along the EastLink tollway early on a Saturday morning in November when his van was sprayed with bullets, killing him.

Paul Virgona was 15 minutes into his drive to work when he was gunned down. ( Fresh State )

Police raided 12 properties across Melbourne early this morning, including Mongols outlaw motorcycle gang clubhouses in Ferntree Gully and Port Melbourne.

Police units including the Special Operations Group also executed warrants at homes in Montrose, Kilsyth, Lilydale, Tecoma, Wantirna South, Southbank, Noble Park and Croydon, and commercial premises in South Melbourne and Port Melbourne.

Aaron Ong, 34, from Kilsyth and Josh Rider, 29, from Port Melbourne have been charged with Mr Virgona's murder.

Victoria Police Assistant Commissioner Tess Walsh told a press conference this morning the two men were "associated" with the Mongols.

She said Mr Virgona had "no criminal associates and no association with the Mongols" but could not say whether the killing was a case of mistaken identity.

Mr Rider and Mr Ong fronted the Melbourne Magistrates' Court this afternoon and sat motionless in the dock as they were told by the magistrate they "obviously" could not apply for bail.

Mr Ong appeared to have a bruise under his left eye.

According to documents tendered to the court, Mr Rider and Mr Ong used a 9mm semi-automatic handgun to shoot 11 rounds into the driver's side of Mr Virgona's van, striking him multiple times.

The documents said the killing involved "a considerable amount of pre-planning" including the use of two stolen cars.

One of the cars was parked prior to the killing in a remote location, where the second car was set on fire.

The gun used in the killing has not been found and police are yet to establish a motive, the documents said.

A property in Port Melbourne was among 12 raided by police this morning. ( AAP )

The pair were remanded in custody to reappear in court in May.

The court was told the two men had "acted in company" to murder Mr Virgona.

Earlier, police also arrested a 30-year-old Montrose man, who was being interviewed by detectives from the anti-bikie Echo Taskforce.

Assistant Commissioner Walsh said this man was likely to be charged with drug and firearm offences.

She said police seized six firearms, a boat and powder that was believed to be drugs in this morning's raids.

Paul Virgona's widow Antonietta and son Luca appealed for information about the killing earlier this month. ( AAP: David Crosling )

Since the shooting, police have focused on a Mercedes with the number plate AZE-110, which followed Mr Virgona from his property and was later set on fire in Mooroolbark, as well as two men who were seen leaving a Volkswagen ute near Bayswater parkland.

Mr Virgona was killed in his van as it emerged from the Mullum Mullum tunnel at Donvale about 2:15am on November 9.

His car came to rest in the right-hand lanes of the tollway, sparking calls from other motorists about a car blocking lanes.

'There are people out there who know why this happened'

Mr Virgona's widow Antonietta and son Luca held a press conference earlier this month to appeal for information about the killing.

Luca Virgona described his father as an honest and dedicated man, whose death had left the family distraught.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 1 minute 35 seconds 1 m 35 s Mr Virgona's son said "hurtful" rumours about the reasons his father was targeted were not based on the facts.

"No amount of effort, pleading or goodwill can bring him back and the shock of his absence will never cease as it's now embedded firmly in our daily lives," he said.

"There are people out there who know why this happened to my father.

"All I ask is that anyone who has information come forward to help us find some sense of justice in a situation where there is none."