A major review has been launched by Healthcare Inspectorate Wales.
Pharmacists are concerned that fewer than half of them are involved in combating misuse, meaning that services are "patchy" across Wales.
Cath Savage, Welsh director of the Royal Pharmaceutical Society of Great Britain, said: "It is important that patients do not get fragmented over bureaucratic service and the expertise of all health professionals is used to the full. With prevention being a priority for the Government, pharmacies are well positioned to play an important role in public health campaigns.
"In addition, pharmacists across Wales have an acknowledged history of delivering support services for substance misusers.
"Syringe and needle exchange services as well as supervised administration of medicine services are provided by pharmacists. However, with less than 50% of pharmacists currently being commissioned to provide these services, the availability of these services is patchy across Wales."
The HIW review will study the planning, commissioning and delivery of treatments that involve prescribing drug substitutes such as methadone.
It will focus on the experiences of the users of the services and the outcome of the treatments, as we well as the quality of management.
The review will also study waiting times, how users are referred for treatment and whether help was provided in areas such as housing, employment and training.
Brian Gibbons, the Minister for Social Justice and Local Government, said: "A major aim of the substance misuse strategy I launched last week is to continue to improve treatment services across Wales.
"This series of reviews will help us find out what is working well and ensure that services across Wales learn from each other."
Pharmacists are asserting they must be at the heart of the Assembly Government's strategy to tackle substance misuse and hope the government would come round to accord them their due place in the campaign.