Elective surgery patients are waiting up to several years on hidden waiting lists to see specialists in hospital outpatient clinics, the Australian Medical Association says.

Elective surgery patients can be referred to see a specialist in a public hospital outpatient clinic, or in a private clinic where they generally have to pay out-of-pocket ahead of joining elective surgery wait lists.

There is no reliable national data on how long it takes patients to see a specialist in an outpatient clinic but it can be years, AMA president Professor Steve Robson said on Friday.

"These hidden figures are a scandal that affect hundreds and thousands of patients and impact a health system already in logjam, including general practice that has to deal with the pressure of looking after many of these patients in the meantime," he said.

"Elective surgery waiting times are reported nationally each year, but these numbers don't reflect the time someone waits to see the specialist in an outpatient clinic."

Public hospital outpatient appointments are scheduled by levels of urgency.

Specialist consultations are recommended within 30 days for the most urgent patients and 365 days for the least urgent.

The limited data available shows many states are falling short of the performance targets, according to an AMA report launched on Friday.

Patients requiring urgent neurosurgeon appointments can wait up to 930 days in Victoria, and for an ear, nose and throat appointment the wait can be more than 1400 days.

Victorian Health Minister Mary-Anne Thomas acknowledged the long wait times were very distressing for patients but said the problem wasn't unique to the state.

"The COVID pandemic has had an incredible impact on the capacity of our health services and our health professionals to deliver the care that people need and expect," she told reporters.

In Queensland, the wait for an ear, nose, and throat appointment can be nearly 700 days, and the wait for an urgent gastroenterology or rheumatology appointment is more than 150 days.

About 250,000 patients in Queensland were waiting for appointments at hospital outpatient clinics, Prof Robson said.

Patients waiting to see a specialist to get them on the official surgery waiting list often develop other health issues during that time, costing the system more.

"The only way we can fix our hospital system is by having total transparency on the number of people who are waiting for care - this means counting people from the time the general practitioner refers them to a specialist," Prof Robson added.

While the AMA couldn't nail down just how many patients were on hidden waiting lists, it said thousands of them were becoming so unwell while waiting they ended up in emergency care.

"We're seeing it in emergency departments every day," representative Dr Sarah Whitelaw said.

Patients were unable to make an informed decision about whether to go through the public or private system when they didn't have the full picture of waiting times, the AMA said.

The Australian Institute of Health and Welfare is working with jurisdictions toward publishing outpatient waiting times in the future but the AMA said a national recovery plan is needed to improve wait times for outpatient appointments and elective surgeries.

It's pitched a new health funding agreement with the federal, state and territory governments, increasing the commonwealth's contribution to 50 per cent for activity and abolishing the 6.5 per cent annual funding rise cap on public hospital services.