Among the affected areas are Canberra, Queanbeyan, Newcastle, Maitland and Geelong.

The ACT already has the lowest rates of bulk billing in the country and the changes have led to fears more practices will stop bulk billing children, pensioners and other concession patients.

As of January, Canberra and Queanbeyan doctors were not eligible for federal government rural incentives because of a new classification system.

It meant the extra payment to bulk bill children and concession patients fell by 34 per cent from $9.65 to $6.40.

While the federal opposition has welcomed the new classification system because it better targets rural and remote areas, opposition Health Spokesman Chris Bowen said he was alarmed at the consequences it was having in areas like Canberra.

Canberra GP and Australian Medical Association ACT branch president Antonio Di Dio said some Canberra practices had become reliant on the incentives even though they could not be considered rural.

"Our view is that they never should have been forced to be in this position," he said. "They would not have been if some major aspects of general practice funding had not been frozen for so many years.

"The pleas from practices that are losing the incentive simply highlights the need for general practice to be funded properly."

Royal Australian College of General Practitioners ACT and NSW chair Charlotte Hespe said the college backed the classification changes.

But she said the effect on Canberra practices showed there needed to be more active campaigns for higher medicare rebates to make bulk billing more viable.

"Until we address the issue of funding and say payments need to be more appropriate, we're not going to solve the problem," Dr Hespe said.

Mr Bowen wrote to Health Minister Greg Hunt asking him to consider mitigating the impact of the changes.

"Many affected practices say this will force them to stop bulk billing children, pensioners and other concession patients," he said in the letter.

"In some cases, practices have warned that the change will render them unviable altogether. This is alarming in all affected areas, particularly in areas of socioeconomic disadvantage."

A Department of Health spokesman said the rural incentives were based on outdated 1991 population statistics.

"This update is about ensuring incentives are correctly targeted to practitioners working in regional, rural and remote areas, rather than in metropolitan areas or larger towns," he said.

"The update aligns the geographic eligibility for rural bulk-billing incentives with other health programs and ensures the latest data is used in our programs.

"The Government is investing an additional $1.6 billion to strengthen primary care. This includes the reintroduction of annual indexation of all GP Medicare items effective July 2019, increasing the level of financial support that patients receive for these services."