Professor Brendan Murphy, Chief Medical Officer for the government, has refuted claims a cheap vaccine failed to protect the elderly in what has been Australia's worst flu season on record.

Figures reveal more than 217,000 Australians had laboratory confirmed cases of the flu this year - more than double the previous record of just over 100,000 in 2015.

Despite a horror flu season, Professor Brendan Murphy said the claims Australia used a "cheap vaccine" were "utterly false" and stood by the immunisation being used around the world.

"The flu vaccines chosen this year were the best available in Australian market, selected by medical experts in Australia and around the world," Professor Brendan Murphy said in a media statement.

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"They are the same vaccines which are available and used in the UK, US and other countries and the same vaccines available on the private market in Australia.

"The two vaccines mentioned in the media today are not available in Australia because the companies have not had them registered for use in Australia with the Therapeutic Goods Administration.

"They have, therefore, not submitted an application for their use on the National Immunisation Program with the Pharmaceutical Benefits Advisory Committee (PBAC)."

"A vaccine cannot be considered by the PBAC, unless a company submits an application and the vaccine has been approved for use in Australia by the Therapeutic Goods Administration. "

Seqirus, a vaccine manufacturer in Australia, called claims that a better immunisation was available on the market as "grossly misleading".

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"Claims made in the media today that an enhanced influenza vaccine was available and not selected by the Federal government for the 2017 influenza season are incorrect and grossly misleading," a statement from Seqirus read.

"Australia has one of the most sophisticated and integrated national immunisation programs in the world. Seasonal influenza vaccine is provided on the Australian Government’s National Immunisation Program (NIP) at no-cost to at-risk members of the community including for persons aged over 65 years.

"In 2016, the Australian Government was the first in the world to exclusively offer quadrivalent (four strain) influenza vaccination for the National Immunisation Program, superceding trivalent (three strain) vaccines."

In a press conference, Professor Murphy said the influenza A strain underwent change throughout the season resulting in the elderly responding poorly to the flu.

"Another very important factor this year was the nature of the predominant influenza A strain, which is a virus that did seem to undergo some change during the year, and generally vaccine protection was less across the whole community for this strain," he said.

"So the elderly had a double impact, as you might think, from a virus that changed a bit and, generally, they have a weaker immune response."

Influenza expert Professor Paul Van Buynder, chair of the Immunisation Coalition, says stronger vaccines are available overseas but because of licensing issues and the purchasing process they could not be accessed here.

"We didn't have a choice to get the better one," Prof Van Buynder said.

The vaccine that was used, however, did not protect the elderly effectively and was partially to blame for more than 500 flu-related deaths this year, Prof Van Buynder said.

"There was a range of strains circulating and that's really what did the damage. We had new viruses, we had lots of children spreading viruses and we had no protection in the elderly from the vaccine itself," Prof Van Buynder said.

For supply through the NIP the vaccines need to be registered by the Therapeutic Goods Administration and recommended by the Pharmaceutical Benefits Advisory Committee (PBAC) based on strain advice from the World Health Organization.

Professor van Buynder works as a public physician on the Gold Coast and has worked as a member of an expert panel to help the government choose the vaccine for national immunisation.

The Australian Influenza Surveillance Report showed notification rates have been highest for adults aged 80 years or older, with a peak also amongst children aged five to nine-years-old.

Influenza A was the most common virus throughout the season.

- With AAP