As pharmacists prepare to take on more medical work under a multi-billion dollar deal with the federal government, President of the Royal Australian College of General Practitioners, Frank R Jones, said baseless homeopathic treatments should not sit alongside conventional medical treatments in retail pharmacies.

"We would certainly encourage our pharmacy colleagues to really critically look at what they are selling at their chemists," he said.

"I think they are very, very conflicted and I think really if they are on board with the rest of the medical community, they have to practise evidence-based medicine."

As the College of GPs launched an advertising campaign this week to raise their profile and highlight their qualifications, Dr Jones said pharmacists were selling "a lot" of products that were not evidence based, meaning they lack scientific proof of efficacy or have been proven not to work.

"We know a lot of cough medicines for example make very little difference … [and] I still see occasionally that they are in chemist shops," he said. "They [pharmacists] have to either practise scientifically or not."

The College of GPs campaign – a TV and cinema advertisement that spruiks the benefits of having an ongoing relationship with a GP – comes after the federal government's failed attempt to introduce a new co-payment for GP consultations, and the continuation of a controversial freeze on indexation of medicare funding for their services.

It also follows federal Health Minister Sussan Ley's announcement last month that pharmacists could start receiving funding to perform work currently done by doctors and nurses, such as vaccinations, wound care and management of conditions such as arthritis. The government has provided $50 million for a trial, but the details are yet to be determined.

Pharmacists have previously proposed offering checks for weight, blood pressure, blood sugar and cholesterol, sparking concern among some doctors that they are moving into their territory without adequate qualifications.

In response to a recent National Health and Medical Research Council review that showed homeopathy was useless, Grant Kardachi, the President of the Pharmaceutical Society of Australia (the peak professional organisation for pharmacists) said it highlighted the need for pharmacists to advise consumers of the dangers of choosing homeopathy over evidence-based medicine.

"Clearly under the PSA Code of Ethics pharmacists must caution against the use of homeopathic products," Mr Kardachi said in March.

But a spokesman for the Pharmacy Guild of Australia (the peak body representing pharmacists with retail stores) said the guild does not tell pharmacists what they should and should not stock.

However, its policy on complementary medicines states that pharmacists should be aware of "the efficacy and safety of complementary medicines sold within their pharmacy, using an evidence-based approach and utilising available clinical / traditional-use information".

The guild's policy says consumers should have access to trained staff who are aware of the different levels of evidence for such products, so they can make an informed choice. Pharmacists should also be aware of the "placebo effect" and provide advice to consumers about the risks and benefits of their options.