MORE than $28 million will be ripped out of Victoria's rural health system following changes to federal funding.

The Australian Medical Association, rural hospitals and the Opposition have slammed the cuts, which include some money already spent last financial year.

Commonwealth public hospital payment to state governments under the National Health Reform Agreement is set to be reduced after adjustments to population estimates and a health cost index.

According to the new calculation Victoria will lose $106.7 million - $28.7 million of which will affect all 69 rural and regional health services across the state.

The worst-affected regional services will be Geelong's Barwon Health, which will lose $4.9 million, the Bendigo Health Care Group ($3 million), Ballarat Health Service ($2.9 million) and Traralgon's Latrobe Regional Hospital ($2.2 million).

Smaller and more remote health services such as Dunmunkle Health Services, Ouyen's Mallee Track Health and Omeo District Health will all wear cuts of about 1.5 per cent.

Federal Health Minister Tanya Plibersek admitted Victoria's funding under the formula would be reduced, but state Health Minister Davis David had agreed to the arrangement.

She said Commonwealth funding would not grow as fast as expected because of the state's population and health costs had not increased as much as anticipated.

"But (Commonwealth funding) will still grow by $900 million or 26 per cent," Ms Plibersek said.

Federal Opposition health spokesman Peter Dutton met with chiefs from Warrnambool and Hamilton hospitals to discuss the issue.

Mr Dutton said the decision to make the cuts part way through the financial year was a disgrace, but would not commit to reinstating the money if elected to Government.

"The biggest issue is to fight these cuts, because they are in this financial year. Doctors have already been contracted, and patients will be turned away," Mr Dutton said.

AMA Victorian president Stephen Parnis said the cuts would affect patient care.