McKenzie Davey Pharmacy pharmacist Anand Raju said they were waiting for back orders to be filled.

"We ran out last week but still have some for the over 65 government supply," he said. "Our timeframe for a new order was the end of this week but it will depend on when they are released."

At Thomas and Chong Pharmacy, pharmacist Charles Wong said they were also waiting for new stock.

"We're not sure if we will get any," he said. "I heard there had been an increase of 20 to 30 per cent in people wanting them. We didn't expect to run out so quickly. They have run out (in previous) years but never in May."

UFS View Street pharmacy manager Kirrilee Miller said they got a fresh order of vaccines in this week but had sold them all to people on a waiting list.

"People are clearly aware of how important (the flu vaccine) is," she said. We have a few government stock vaccines left but that will be gone in the next day or so.

"We also have some on back-order with the supplier but when that comes, we're not sure."

So far this year, there have been 13,133 cases of laboratory-confirmed influenza, compared to 2,268 cases for the same period last year. There were a total 11,607 cases in 2018.

"We've seen a higher than usual start to the flu season and tragically, we know that flu can be deadly," state minister for health Jenny Mikakos said.

"That's why we've ordered record amounts of vaccinations for Victorians who qualify for free immunisations under the National Immunisation Program."

"We are confident that we have supplies to ensure these vaccinations are available for groups who are eligible for free vaccinations. The Department of Health and Human Services will closely monitor whether more are needed."

EARLIER: Bendigo pharmacies are struggling to meet the demand for flu vaccines as winter approaches.

The vaccination shortage comes after chemists saw a huge demand for the vaccination in the lead up to colder weather.

Pharmacist in charge at Priceline Pharmacy Bendigo Marketplace Long Nguyen said staff were taking dozens of calls a day from people looking for the vaccine.

"We have completely run out. I have heard UFS Pharmacies, White Hills Amcal and Chemist Wares are all also out (of stock)," he said.

"I can't say 100 per cent (that more vaccines will be stocked). We have contacted the manufacturer trying to get more stock, but at this stage they don't have a date for us."

A staff member at Chemist Warehouse Bendigo confirmed they were out of flu vaccines.

Some doctors and some pharmacies still have stock for people who are eligible for the state government's free vaccine program.

Those people include children aged from six months to under five years, Victorians aged over 65, pregnant women, Aboriginal and Torres Strait Islanders and anyone with a chronic condition or weakened immune system.

Mr Nguyen said there was usually a shortage of vaccines at this time of year.

"Every year this happens," he said. "We've been referring people to smaller, independent pharmacies. Stocks usually run out from the bigger chain first, then the smaller pharmacies.

"For people eligible for the free vaccine under immunisation program, we still have stock."

White Hills Amcal owner Sanjay Jhaveri said his store had run out of vaccines.

"We sold our last one today. There has been a huge demand for them," he said.

"I believe it could be another month before we get more in. We are also out of the free vaccines (for the immunisation program). We have run out of everything in terms of the flu vaccine."

Mr Jhaveri said White Hills Amcal administered vaccines in the pharmacy.

"We have done about 100 in the last week and had to turn quite a few people away," he said.

"I think the advertising and the stories in the news has really hit home this year. More so than before."

Bendigo Primary Care Centre chief executive Glen Careedy said his organisation ran out of free immunisation program vaccines for a few days as well.

"A couple of weeks ago for about three days we ran out of one type but we have generally been able to keep up with demand.

"The biggest problem isn't the vaccine. The doctors are getting hammered, so getting an appointment is the hard part."

Mr Careedy said Bendigo Primary Care was prepared for a big influx.

"We see about 8000 people a month and this year have been served really well with the (government supply) of vaccine," he said.

READ MORE: 2018 - Victoria: Demand for influenza vaccine stretches supplies

READ MORE: 2018 - Victorian health minister says the supply of influenza vaccine needs to be improved

Federal health minister Greg Hunt said Australia had ordered an extra 400,000 vaccines to meet what he said was an unprecedented demand.

"I have been working with vaccines companies to ensure that there is sufficient supply in the private market," he said.

"This will take the overall number of flu vaccines available in Australia this year to over 12.5 million an increase from 11 million in 2018."

More than 12.1 million flu vaccines have been released into the Australian market, with 7.5 million allocated to government vaccination programs and 4.6 million doses available for the general population.

Mr Hunt said supplies for federal and state National Immunisation Program programs were secure.

The Victorian Department of Health and Human Services said there was high demand for the free vaccines.

"The Victorian government expects to make more than two million doses of vaccine available to those eligible for free vaccinations," a DHHS spokesman said.

"Pharmacies and other immunisation providers also source flu vaccine from the major pharmaceutical companies for people who are not eligible for the Government sponsored free program."

Mr Nguyen said if people missed out on a flu vaccine they should be aware of their hygiene in an effort to avoid getting sick.

"General hygiene practices can (help reduce) the chance. So coughing into your elbow, washing your hands (regularly) and cleaning things like the handle of your shopping trolley," he said.

"You can improve your immune system by eating more fresh fruit, appropriate vitamins and supplements. Also if you hear people coughing, it is best to try and avoid contact and be mindful of what's happening around you."

- with AAP

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