Dr Roy Robertson’s call has drawn sympathy from one of Police Scotland’s most senior drugs officer who has stressed the importance of engaging with addicts.
But any change seems some way off as drug laws are reserved to Westminster and the Home Office has no imminent plans to change policy.
Scotland has the highest number of drug deaths in the European Union.
Dr Robertson, a professor of addiction medicine at Edinburgh University and former Home Office adviser, said radical changes were needed to stave off an “epidemic” among users.
“I do think we are moving towards an area where politicians and policy makers are going to start talking seriously about a new structure to control drugs, which allows for the fact that we really don’t want to just put people in jail for the possession of drugs that they have for their own personal use,” he told BBC Scotland.
“What we have to do is start from the point of view that we do want to make change and how we’re going to do it.
“We need to start building a new structure before we take away the old structure.”
A Royal Commission should be established to look at new legalisation, the medic added.
Countries like Portugal do not prosecute those caught in possession of small quantities of drugs.
Det Insp Allan Elderbrant, the head of substance misuse at Police Scotland, indicated he would back changes allowing officers to refer people directly to health services rather than the courts. He said: “If that opportunity was afforded to us and if that change did come, then yes, that’s probably the route that we would go down.”
A Home Office spokeswoman said the UK government’s approach was in place “to prevent drug use in our communities”.
She added its comprehensive drugs strategy set out a balanced approach that “brings together police, health, community and global partners to tackle the illicit drug trade, protect the most vulnerable and help those with a drug dependency to recover and turn their lives around”.
Recent proposals to introduce so called “fix rooms” in Glasgow, where addicts could inject without fear of repercussion, were rejected when the UK government ruled out the plans.
Public health minister Aileen Campbell said there was a need to look at “innovative solutions and bold ideas” to tackle the problem.
Liberal Democrat leader Willie Rennie said: “It is time for a sensible and enlightened new approach to address the damage that drugs inflict on our communities, families and individuals. We need a policy that prevents unnecessary deaths, alleviates the burden on our NHS and frees up the justice system to tackle the people and organised crime groups producing and dealing drugs.”