Two men charged with drug trafficking, and who have links to outlaw motorcycle gangs, had been staying at a Port Melbourne home owned by former AFL coach Mark Thompson, the ABC understands.

A 31-year-old man from Lara, near Geelong, and a 28-year-old Port Melbourne man were remanded in custody after being charged with drug trafficking on Tuesday.

The ABC understands those men were Karl Holt, who has connections to the Bandidos bikie gang, and Thomas Windsor, who is affiliated with the Rebels bikie gang.

Thomas Windsor was remanded in custody after being charged with drug trafficking. ( Facebook: Thomas Windsor )

Neither of them are patched members.

It is understood the pair had been staying at a Port Melbourne property owned by Thompson, which was raided by police last Friday.

Thompson was arrested and went to a police station to be questioned by appointment on Tuesday, but was released without charge.

A 22-year-old Mill Park woman was also arrested and charged with drug trafficking in connection with the investigation.

Mr Thompson was released without charge after being questioned. ( AAP: Joe Castro )

All three will return to court at a later date.

Thompson, a two-time Essendon premiership player and former captain, was an assistant at the Bombers under James Hird at the time of the disastrous supplements program.

The AFL fined him $30,000 for his part in the saga, but Thompson took over the senior role at Essendon for one season in 2014 while Hird served a 12-month suspension.

From 2000-2010 Thompson was the senior coach at Geelong, winning two premierships in a dominant era for the Cats.