Nicole Higgins from the Royal Australian College of General Practitioners seized on the study to claim vindication.
"Late last year, the entire general practice profession was slandered by baseless claims of 'rorting' for no good reason," Dr Higgins said.
"We have been vindicated and we await an apology."
Referring to a study released by researchers at the University of Sydney, Dr Higgins said GPs were under-billing by $350 million a year.
"GPs are shouldering a huge burden," she said.
"Give us a break. For those who got it wrong, an apology is in order to all the hardworking GPs out there."
Allegations of $8 billion in rorting were first aired by compliance consultant and lawyer Margaret Faux and later reported in the media.
An independent review by former senior health bureaucrat Pradeep Philip had found the claims were not supported by evidence.
Dr Higgins said the debunked claims had caused immense harm to the 27,000 GPs working across Australia.
"It's just another kick in the guts," she told AAP.
"It significantly reduced morale at a time when general practice is underfunded and undervalued.
"The issue is with the system and not the GPs. The government needs to simplify the system and ensure we have a focus on education and not punitive measures."
The college's chief executive Paul Wappett said the independent review confirmed Medicare was no longer fit for purpose.
"It's not providing a sufficient safety net to those who can't afford healthcare at the cost it takes to deliver it," he said.
"It's unnecessarily complex, making compliance by GPs difficult, enforcement by regulators onerous, and understanding by patients and the community nigh-on impossible."
Almost 3000 GPs were surveyed for the University of Sydney study, with almost 85 per cent reporting undercharging Medicare for at least one consultation.
Researchers estimated the undercharging by GPs saved Medicare $352 million across 90,000 consultations in one financial year.
The study published in the Australian Journal of General Practice also found GPs undercharged about 12 per cent of total consultations and only overcharged 1.6 per cent.
"Our study has shown that GPs are more likely to err towards undercharging than to overcharging," lead author Christopher Harrison said.
"This contrasts with previous research and reports alleging widespread fraud related to GP billing of Medicare.
Dr Harrison said general practice was in crisis.
"Allegations of fraud have been damaging to a workforce that is struggling to attract medical graduates to general practice."
Dr Harrison said a major reason why GPs undercharged - even for long consultations - was the fear of being audited.
The paper analysed data from a national study of GP clinical activity in Australia that ran from 1998 to 2016, concentrating on the years 2013 to 2016.
Each year, a different group of 1000 GPs recorded information about their consultation sessions for 100 consecutive consenting patients.
The data was used to calculate the cost differences between the Medicare Benefits Schedule items charged and the items that could have been charged based on the length of the consultation.
The federal government is working with the states and territories to overhaul the Medicare system.
Prime Minister Anthony Albanese has declared better policy, not necessarily more funding, would be key to the reforms.
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