Strathclyde Chief Constable Campbell Corrigan and British Transport Police's Scottish commander Ellie Bird both raised the issue after concerns were raised by frontline officers.
The force, however, is not echoing criticism of treatment using the heroin substitute made by Conservatives in recent years.
Ms Bird's force polices Glasgow Central Station, which has a busy chemist that distributes methadone.
She said: "While I recognise the needs, and support its provision for those on the methadone programme as part of their structured rehabilitation plan, I would suggest there is a real need for a much wider debate involving all those involved and support the notion of administering this in a more suitable environment."
Mr Corrigan said: "I am not sure that city-centre chemists are the best places to distribute methadone.
"It would seem more appropriate to offer this facility at hubs away from the city centre where people can access a range of other services, such as help for their children.
"This would mean there would be less of an impact on others and perhaps reduce the stigma around those who use the service."
Frontline police sources stress they are concerned about how they manage the complex mix of drug users, families, commuters and rail and road traffic near busy dispensing chemists. The number of people caught in possession of drugs in parts of central Glasgow doubled in 2011/12 – but remains far lower than five or six years ago.
Police have no complaint, however, about the management of pharmacies.
Iain Brotchie, spokesman for the Royal Pharmaceutical Society in Scotland, said: "It's important to understand why offering methadone dispensing in city-centre pharmacies is a good idea.
"Many drug misusers are trying to get their lives back together. They might not want people in their own community seeing them going to get their methadone.
"Other drug misusers will need a city-centre pharmacy to dispense their methadone if they are trying to hold down a job as they battle their addictions.
"Of course, some drug misusers will live in the city centre as well, and they want to get their methadone from a convenient pharmacy."
A spokeswoman for the Scottish Drug Forum said: "The reasons why vulnerable people with drug problems gravitate towards the city centre are multiple and underline the issues that lie behind problematic drug use – such as homelessness, mental health and social isolation.
"Giving people with drug problems quick and easy access to treatment and care is of key importance which is why services are normally clustered in areas where drug users frequent."