Mark Benjamin, 53, was granted bail at the Bendigo Magistrates' Court on Wednesday while facing charges of trafficking, use and possession of methamphetamine.

A woman was also charged after a raid at the property on Tuesday.

First Constable Wendy Turner told the court a mobile phone found at the property contained messages relating to the sale of ice, but the owner of the phone had not yet been identified.

She said police had fears Benjamin could have been driving trains under the influence of ice, after police found a pipe in the accused's bedroom.

Defence counsel Luke Docherty said police had not connected the discovered drugs to either of the accused and the owner of the phone was also unclear.

The bag that contained the drugs had not been seized by police.

Magistrate Jennifer Tregent said the case against Benjamin was not the strongest at this stage and questioned why police had not seized all relevant property found during the raid.

She said it was unclear what V/Line's drug testing policies were.

"With so much ice out there, there should be some form of testing. But finding out if he was driving trains while using isn't really an option yet," Magistrate Tregent said.

"It would be very easy for police to obtain another warrant for your residence. Hopefully this experience has frightened you."

Benjamin is the primary carer for his elderly mother at their Long Gully home.

Benjamin will undergo weekly drug testing and cannot own a mobile phone as conditions of his bail.

He will reappear in court on April 2.