V/LINE stood down a train driver with full pay after he was allegedly found in possession of about $10,000 in the drug ice during a raid on a Long Gully property in March.

Mark Benjamin, 53, appeared for a second time in the Bendigo Magistrates Court on Thursday where he applied to have his bail conditions altered.

He faces six charges including trafficking, use and possession of methamphetamine following the raid on March 3.

Police found the amount of the drug ice inside a women's carry bag, and hidden in other items in the accused's bedroom, along with a pipe for smoking methamphetmine.

The co-accused is a female who was in a defacto relationship with Benjamin.

Conditions placed upon Benjamin by Magistrate Jennifer Tregent included that he not be allowed to possess a mobile phone unless it was for work purposes.

Benjamin's solicitor Serge Petrovich questioned aspects of the evidence against his client and doubted whether there was a need to seize all three mobile phones taken during the raid.

He said as the full time carer for his elderly mother, Benjamin needed to have a phone to carry out his carer duties.

"Even if he speaks to a solicitor on his mobile phone, he is in breach of his bail conditions," Mr Petrovich said.

"My argument is based on the strength of the case, vis-a-vis the need for phones to be kept as part of the prosecution case."

Police informant Constable Bianca Cola said there was evidence on all three phones seized that pointed to ice dealing, along with the co-accused.

She said given Benjamin had been stood down by V/Line, there was no need for him to possess a phone.

"He does not need a phone until these matters have been settled in court," Constable Cola said.

"We don't know specifically who sent each message from the phones, but we can assume they were sent by Mr Benjamin because each of them was activated by his email account."

Magistrate Jonathan Klestadt denied the request for Benjamin to possess a mobile phone.

Benjamin will re-appear at the Bendigo Magistrates Court on April 30 for a contest mention hearing.