In some cases, GPs' surgeries and pharmacies have been adding patients' names to waiting lists until supplies become available.

Wagga pharmacist Luke van der Rijt said demand for the flu vaccine had been extremely high this year.

"It has put a big dent in supply," Mr van de Rijt said.

He said doctors and pharmacists pre-ordered their supplies of the vaccine well in advice of the traditional flu season, but this year, demand has exceeded anticipated demand.

In one instance of increased demand, the Murrumbidgee Local Health District requires that anyone visiting an aged care facility provides proof of a 2020 vaccination for flu.

The federal government announced in April that it had ordered three million additional doses of flu vaccine, bringing the total number of doses available for Australians to 16.5 million.

These additional doses will be available through pharmacies and GPs and are expected to continue to be delivered between now and June.

Mr van der Rijt encouraged Wagga people who had not yet had their vaccination to check with their GPs and with the city's pharmacies about availability.

Wagga GP Ayman Shenouda said vaccines were being delivered in batches to the Glenrock Country Practice, where he is based, and patients' needs were being handled accordingly.

"We have immunised the majority of our patients, but we still have a few to immunise," Associate Professor Shenouda said.

"It's not a steady supply flow, but it comes in batches and we manage that as a practice to make sure that our patients are immunised."

Harry Nespolon, the president of the Royal Australian College of General Practitioners said doctors had seen a "welcome" increase in demand for the flu vaccine because of the COVID-19 pandemic.

"The RACGP and government have been encouraging people to get their vaccine earlier than usual to ensure that the health system doesn't have to deal with hospitalisations for the flu at the same time as managing COVID-19 patients," he said.

"The vaccine is being rolled out across the country. It is a massive logistical exercise and the RACGP has heard reports from GPs that they haven't received enough stock and they are understandably very frustrated.

"It is unacceptable that clinics don't have enough stock, we need patients to get their flu jabs as soon as practicable. We are listening to the concerns of GPs during this difficult time and urge health authorities to do all they can to ensure GP clinics have enough vaccinations for their patients."