Some hospitals may also be set to lose organ transplant services to other hospitals so the state can cut costs and streamline the system.

The shake-up in coming months is likely to be controversial for specialists who pride themselves on working in centres of excellence, but it is unlikely to reduce the number of transplants being done.

The chair of the Victorian regional committee of the Royal Australasian College of Surgeons, Dr Robert Stunden, said although every health network would deal with budget cuts differently, previous experience showed the first thing to go was elective surgery.

The paediatric surgeon at several Melbourne public hospitals said semi-urgent or category two elective surgery lists could be cut in half over the next six months, meaning people who should be operated on within three months could expect their wait to at least double to six months.

Category two patients are defined as those with ''some pain, dysfunction and disability'' and include people waiting for hip or knee replacements and vascular surgery.

Dr Stunden said that although urgent surgery was likely to still be done on time, no surgical specialty, including cancer and paediatric care, would be immune from cuts, meaning many patients could expect to wait longer in pain.

''We are expecting to have major cutbacks in lists over the next six months … waiting lists will explode,'' he said, adding that it was ''terrible'' for patients. ''The quicker we can manage these patients, the better it is for them.''

Dr Stunden said some hospitals were considering delaying new programs in the new year while others were discussing the streamlining of ''super-specialised services'' such as transplant surgery, so instead of three hospitals doing liver transplants, for example, only one would. This would cut the cost of having three hospitals set up for the procedure.

While this would upset some doctors in the field, Dr Stunden said it did not mean the number of procedures would be cut back.

''There will have to be some give and take in the major institutions for the benefit of the community as a whole,'' he said.

Most transplants are currently done at Monash Medical Centre and the Alfred, Austin and Royal Melbourne hospitals.

Victorian Health Minister David Davis last week told hospitals to plan for multimillion-dollar budget cuts over the next seven months. He blamed the federal government for refusing to back down on plans to slash $106.7 million from Victorian hospital budgets this financial year.

Mr Davis said the federal government's recalculations of its funding were based on flawed population data. However, the federal government disputes this and says funding to the state is still increasing compared to last year.

On Tuesday, the Australian Medical Association and the Australasian College for Emergency Medicine condemned the budget cuts, saying public hospitals were already overwhelmed.

''The cuts must stop - the public hospital system has nothing more to give,'' said AMA president Steve Hambleton.

Elective surgery waiting lists have increased in Victoria over the past two years. At the end of June, 46,131 people were waiting for surgery - up from 37,194 in June 2010.