The Pharmacy Guild of Australia says its deal to promote Blackmore complementary medicines has been withdrawn because of "ill-informed and inflammatory" community outrage.

The deal, denounced by both the Australian Medical Association and the Pharmaceutical Society of Australia, involved pharmacists receiving computer prompts to promote Blackmores supplements when selling certain prescription drugs.

"The last thing the guild would ever want to do is deplete the credibility of community pharmacists or damage the trust in which they are held by Australians," the guild said in a statement.

"It is overwhelmingly clear that the public perception of this endorsement was damaging to the reputation of community pharmacy."

Blackmores CEO Christine Holgate was widely criticised for suggesting the deal meant pharmacists could offer "Coke and fries" upgrades when selling prescription drugs, but she said her comments were taken out of context.

Sorry, this audio has expired Pharmacy Guild withdraws from controversial agreement ( Stephen Dziedzic )

"It is not about up-selling. This is about selling appropriate products to consumers," she said.

Dr Ken Harvey, adjunct senior lecturer of public health at La Trobe University, told ABC News Online the deal was a conflict of interest.

"The guild represents pharmacy owners; they've always seemed to be more concerned with profits than good pharmacy practice," he said.

Dr Harvey says the supplements would have been offered to treat the side effects of drugs including blood-pressure and lipid-lowering medications.

But he says these side effects are uncommon, and there is little or no evidence the supplements are effective in treating them.

"It is true that sometimes people on lipid-lowering medications can get muscle aches and pains, for example," Dr Harvey said.

"But the evidence for taking supplements like coenzyme Q10, which was recommended ... the evidence that this would eliminate the problem is not good.

"Certainly the evidence that taking it routinely will prevent the problem - there's no evidence at all."

Dr Harvey says the National Prescribing Service - an independent authority that advises doctors and pharmacists on treatments - has recently released a review confirming that the routine use of the four complementary medicines included in the Blackmores deal is not recommended.

But the guild says the professionalism and judgment of pharmacists would not have been affected by the deal.

"There is not now and never would be any direction from the guild for pharmacists to be involved in unprofessional, unethical or clinically unsound conduct," it said.

"The idea that community pharmacists would take part in commercial 'upselling' without regard to their professional standards is offensive to our profession and rejected by the guild."

The ABC reported last month that no payment was received by the guild, but that its subsidiary Gold Cross would likely receive payment from Blackmores for endorsing the four companion products with the Gold Cross logo.

Dr Harvey notes that while pharmacists would have been pressured to sell complementary medicines, this does not mean they would have; he notes many pharmacists came out against the deal, as did their representative body.

He says the controversy over the Blackmores deal has thrown light on a wider problem - the lack of understanding about how complementary medicines are regulated.

A total of $1.2 billion worth of complementary medicines - including vitamins, minerals, herbal, aromatherapy and homeopathic products - was sold in Australia last year.

Dr Harvey says while some of these products are evidence-based - like fish oil for treating high lipids - they nevertheless are held to lower standards than prescriptions.

"Prescription medications are very thoroughly evaluated before they are allowed on the market - for quality, safety, and efficacy to make sure they work amongst other things," Dr Harvey said.

"Complementary medicines aren't. It's a trust-based system in which the sponsors basically put their own products on the Australian Register of Therapeutic Goods.

"They tick a box saying that they hold evidence to support the claims; they tick various other boxes suggesting that the products only have a limited list of relatively safe ingredients, that they're manufactured under good manufacturing practice etcetera.

"There is absolutely no assessment by the Therapeutic Goods Administration [TGA] of these claims or these products before they go to market."

In 2010, a report released by the Department of Health and Ageing showed that up to 90 per cent of complementary medicines which were reviewed were found to be non‐compliant with regulatory requirements.

The TGA does not prosecute companies for failing to comply these requirements because the cost of investigating outweighs the fines that can be imposed.

"We have a trust-based system that has been shown to fail," Dr Harvey said, suggesting that clear warning labels be added to complementary medicines saying that they have not been evaluated by health authorities.

He says some complementary medicines have been properly evaluated and registered but these are "few and far between".