A new report published on Tuesday found one in five Australian medical experts tasked with deciding which drugs are recommended for use by doctors have undisclosed links to drug companies.

The report’s authors found in most cases the experts in question were simply following the accepted processes and were not deliberately doing anything wrong.

However, they said that very fact meant the processes needed to be strengthened.

Dr Chris Moy, the chair of the Austalian Medical Association’s Ethics and Medico-Legal Committee agreed that the processes needed to be strengthened.

He said a major problem was eminent members of the medical community declaring their conflict of interest but then proceeding with decision making anyway.

“Eminence can not be allowed to compromise evidence," Dr Moy said.

“Very prominent people in an area walk in and say ‘I have a conflict of interest’ and they’re not putting it at the mercy of the committee to then decide what will happen.”

“So it’s up to individuals but also it’s the processes; those committees need clear processes.”

Medical guidelines are relied on by doctors to inform how they treat various conditions, including advice on which drugs work best according to current medical wisdom.

The President of the Royal Australian College of General Practitioners, Dr Harry Nespolon, said most GPs used the guidelines to inform their treatment decisions, but they also took them with a grain of salt.

"It's a perennial problem – the people you want to be writing the guidelines are those who are at the top of their fields, but they're also the people most likely to be called on by pharmaceutical firms  to do research for example," Dr Nespolon said.

"At the end of the day you've got to trust something, and in general practise you'd never see a patient if you spent your time reading the background to every guideline."

For their part, pharmaceutical companies have defended links to medical experts, with Medicines Australia, which represents a number of major drug companies, saying there was nothing untoward in ensuring the best and brightest worked on developing and promoting new treatments.

"Clinical research is costly and time consuming and without the support of pharmaceutical companies, this important research would not be able to be undertaken, or be as comprehensive," Medicines Australia Chair Elizabeth de Somer said.

"Medicines Australia believes that clinical guidelines should always be of the highest integrity, and be based on the latest evidence, and that relationships with industry and clinicians should be disclosed."

The report’s authors acknowledge the data they were working with finished at 2014, and there have been moves to strengthen processes since then.

The AMA itself has updated its advice on how doctors should interact with industry, while the National Health and Medical Research Council has also updated its guidelines.

The NHMRC’s new guidelines were described by the report’s authors as the “strictest in the world” because they recommend there should be no members with conflicts of interest on guideline boards.

The chief executive of the Consumers Health Forum of Australia, Leanne Wells, said if health and research organisations did not strengthen their own processes, consumers would take matters into their own hands.

“All authors at all times should declare relevant interests as a matter of best practice and transparency and public trust,” Ms Wells said.

“There is a growing interest in principles and standards that require greater transparency in the relationship between industry and clinical and/or consumer groups, most recently the Australian Consensus Framework for Ethical Collaboration in the Healthcare Sector – has 60 or so signatories who are now working on an implementation plan.”

Dr Moy said despite the controversy, most medical guidelines were still sound, they just unfortunately had a “question mark” over them because of the conflict of interest issue.

“In general the guidelines are good, they still are going to be reliant on evidence,” he said.

“It’s sad that it’s the case that there is a question mark, but hopefully we can remove the question marks and ensure there’s much more rigorous declaration processes to manage conflicts of interest.”