Wimmera Health Care Group estimates it will be almost $700,000 out of pocket by the end of the financial year because some of the nation's biggest health funds have decided to stop reimbursing public hospitals for the full cost of private care.

The group's finance and corporate services director Mark Knights said before April last year, health funds paid public hospitals almost the full single-room rate recommended by the Department of Health.

But then, Mr Knights said a number of health funds decided to cut costs.

"The health fund reimbursement for surgical or obstetric admissions to private rooms is about $435 a day, which is a difference of about $298," he said.

Medibank Private, Bupa Australia, Australian Health Management and NIB are among health funds refusing to pay the full single-room rate.

Wimmera Health Care Group chief executive Chris Scott said the health funds' decision was now affecting hospital viability throughout the Wimmera and across the state.

"Wimmera Health Care Group has attempted to manage the loss of $690,000 in revenue," he said.

"But this reduction, compounded by the Commonwealth funding reductions and high cost of patient transport, will push the hospital to make changes."

Wimmera Health Care Group stands to lose more than $2 million by June 30, 2016 because of Federal Government health funding cuts. The service is scrutinising which aspects of its business had been underpinned by private health funds.

It has also been forced to review every private patient admission.

Mr Scott said he could not understand why the health funds had differentiated between a private room in a public hospital and one offered by a private hospital.

"We want to alert the public especially the people of the Wimmera and southern Mallee that their health funds are not paying the full private patient benefits for which they are entitled, and are paying a premium for," he said.

"With no private hospital access locally, people are paying health funds for an option they will not deliver."

A Medibank Private spokeswoman said the changes to single-room rates in public hospitals were made because of a significant jump in the number of patients being treated in single rooms.

"The additional charge for single rooms in public hospitals is several times that paid at private hospitals," she said.

"This is a huge concern for both us and our members."