Hospital budget blowouts from the surge in influenza-affected patients has prompted the state government to announce an additional $200 million flu package to help ailing emergency departments across Victoria.

As of Wednesday, there were 356 cases of the flu in Warrnambool, compared to just 25 last year.

There were 18 new cases last week alone.

South West Healthcare chief executive officer Craig Fraser said this year's flu season had put pressure on hospital resources.

"This year's flu season put enormous strain on the resources of both our hospitals," he said.

"Of Victoria's 65,000 lab-confirmed cases so far this year, 104 of these people were hospitalised here at South West Healthcare.

"Another 79 people suspected of having influenza also required hospitalisation.

"This contributed to record 2018-19 Warrnambool emergency department and Camperdown urgent care centre patient numbers, and record Warrnambool Base Hospital inpatient numbers.

"Staff were dedicated to ensuring infection control precautions were implemented that prevented the spread of influenza to other admitted patients, despite limited numbers of single-patient rooms."

There were 88 influenza cases in Glenelg, 141 in Moyne, 136 in Corangamite and 100 in Southern Grampians this year.

Health Minister Jenny Mikakos said on Thursday the funding boost would help emergency departments cope.

The Minister could not say how much of the $200 million would be funnelled to the south-west.

Mr Fraser said South West Healthcare welcomed any government injection of money which supported keeping communities flu-free.

"We continue to dedicate significant resources and energy to tackle this ongoing challenge," he said.

South West Healthcare continues to be impacted by a cyber breach, over three weeks on from the original attack.

Staff are still unable to use internet or emails, with select staff communicating from external email addresses.

The hospital maintains patient services remain unaffected.

Western Victoria Region MP Bev McArthur, speaking in the Legislative Council this week, drew attention to the continued consequences the attack was having on hospitals and medical care in South West Victoria.

"I have been assured by one of these health facilities that all emails have been lost and that there is no email contact available at health services," she said.

"Staff are moving from one ward to another, one office to another, with handwritten notes. All orders for band-aids and bandages have to be done manually - you cannot do it online in any way, shape or form.

"You have got healthcare workers in facilities that are manually walking from one place to another in the hospital to provide handwritten notes to other staff or using their own mobile phone systems to send messages and information about patients."

It was last week revealed that a "phishing" email containing a virus sparked the attack, which was sent to an employee and then downloaded onto the hospital's computer network, providing cyber criminals with unauthorised access.

Ms McArthur said a Colac cancer patient was told by her physician that had she been in hospital at the time of the cyber attack it could have been fatal.

"Had she been in the hospital at the time of the cyber attack she would have died," she said.

"She was fortunate that she was there two weeks previous to that.

"Cases like this cannot be allowed to happen again - what is the government doing to ensure lessons are learnt, and when will they provide the resources necessary to prevent another catastrophic failure."

She said the issue would not simply disappear when systems get back on line, highlighting the backlog of work being generated by the ongoing failure.

"All records are being recorded manually, and all patient records will need to be uploaded at some point. What provision is going to be made for these facilities to manually reload all this data an information," she said.

"What financial support will they get? Because it will be a massive task."

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