The Australian Medical Association (AMA) has accused the Pharmacy Guild of Australia of putting commercial interests ahead of patients' health under a new deal which will see pharmacists prompted to recommend supplementary medicines to consumers.

The guild has struck an agreement with the company Blackmores to promote the company's products alongside certain prescription drugs.

Under the deal, pharmacists dispensing medicines for several common conditions will receive a prompt in their computer system reminding them to promote a complementary Blackmores product.

The AMA says it appears commercial interests are being put ahead of patients' needs.

But the association has previously been accused of doing the same, and the Pharmacy Guild says it is thrilled about the deal.

The guild says the four Blackmores products in the range have been designed specifically to offset possible side-effects of common prescription drugs.

But AMA president Steve Hambleton says the agreement is just an opportunity to up-sell and increase profits.

"We rely on our pharmacy colleagues to actually assist us in healthcare of the patient," he said.

"It is a very good relationship between doctors and pharmacists, and I'd hate to see anything undermine that.

Sorry, this audio has expired Blackmores pharmacy deal ( Barbara Miller )

"That sort of advice from a professional pharmacist will have a great impact on patients and they may well decide to choose those products.

"We know some patients won't even take all of their medicines because of the price - I'd hate to think that they'd substitute one of their prescribed medicines for one of these companion products."

Dr Hambleton says there is potential to sell companion products with around 58 million claims for PBS prescriptions.

"This is a big financial deal. We can't put finances ahead of the health of a patient," he said.

General practitioners are already sometimes prompted by their computer system to recommend certain medicines to patients, but Dr Hambleton says there is a big difference.

"If you had a particular medical problem you may benefit from some medicines to fix that problem," he said.

"Diabetes is a good example. There is a range of medicines that actually improve healthcare for diabetics. They have all got evidence, they are all TGA [Therapeutic Goods Administration] registered, they all can do what they say they do.

"The difference here is we are talking about complementary or unconventional products where the evidence base is much poorer and we need to see the evidence that these products actually do what they say they do and are worth paying for."

Pharmacy Guild president Kos Sclavos was in transit and unavailable to speak to ABC Radio's AM.

A spokesman for the guild said Mr Sclavos was satisfied Blackmores had good evidence to allow pharmacists to make the recommendations.

The spokesman said Mr Sclavos rejected suggestions the deal is commercially motivated.

No payment has been received by the guild, but its subsidiary Gold Cross is likely to receive payment from Blackmores for agreeing to endorse the four companion products with the Gold Cross logo.

The scheme is due to take effect from October 1.