The man, who can not be identified because of a court order, applied for bail at the Ballarat Magistrates' Court on Wednesday, arguing there were exceptional circumstances for his bail.

Police prosecutor Senior Constable Ben Jones said the man was an unacceptable risk of endangering the welfare of the community and committing offences while on bail.

Nominal informant Sergeant Brent McGuire told the court the accused was on two counts of bail pending trial, for charges including trafficking methamphetamine and a drug of dependence.

Sergeant Brent McGuire said police attended a Ballarat address in September and located a glass jar in the freezer containing 94.6 grams of methylamine, a precursor chemical that can used to make illicit drugs, traces of methamphetamine and amphetamine in glass containers and 47.4 grams of liquid containing methylamphetamine in a glass container.

The court heard the accused told police he used methylamine to extract precious metals.

The man is charged with trafficking and possession of methylamphetamine, possession of precursor chemicals and committing an offence while on bail.

Sergeant McGuire said there was an unacceptable risk the accused would commit further offences while on bail and of endangering the community.

"Clandestine laboratories contain highly flammable material and are very unstable. Any clandestine laboratory poses a danger to the community," he said. "The accused was already on two counts of bail, was previously bailed and continued to set up another lab."

Sergeant McGuire said he would not be satisfied with the risk, even if stringent bail conditions were put in place.

Defence lawyer Manny Brennan said the accused's safety was at risk in custody.

He told the court the purity of the illicit substances detected was not yet known and it took two months for police to remand the accused from the time of the search of the house, showing he was not considered a great risk.

Mr Brennan said the prosecution case that the accused was manufacturing methamphetamine was weak and that the accused had been given 24 hours' notice the police would attend the house.

He told the court the Court Integrated Service Program with a comprehension plan for mental health support, and suitable accommodation was available to the accused if bailed.

Magistrate Ron Saines said he did not view the prosecution case as weak as there was evidence of possession of drugs.

In regards to the risk to the accused's safety in custody, Mr Saines said he believed the risk existed whether he was in the community or in the prison system.

"There are serious charges to be determined in court and a serious history. Upon proof of any charges, a significant period of imprisonment is highly likely," he said.

"My judgment is despite the availability of CISP, exceptional circumstances are not made out here. I am not satisfied the risk of further offending can be addressed with bail conditions."

The accused was refused bail and will return to court in May.