A cheap vaccine has been blamed for the number of Australians succumbing to the flu this winter, with more than double the number of confirmed cases.

The federal government's Chief Medical Officer Professor Brendan Murphy has rejected claims a cheap vaccine was used to protect Australians against the flu this season.

The vaccine was the "best" and only one available at the time, Prof Murphy says.

"The claim that cheap vaccines are purchased for the National Immunisation Program (NIP) is false," Prof Murphy said in a statement on Monday.

"The Australian government purchases the best available vaccines for the NIP and the currently supplied vaccines (eg Fluarix Tetra) are also used in the United States, United Kingdom and other developed countries.".

Health experts are calling on the federal government to make sure it accesses new, super strength vaccines to prevent a repeat of this year's deadly influenza outbreak.

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.

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.

Prof Van Buynder says "two super-vaccines" will be available for license next year, adding reliance on the cheaper vaccine would be unwise.

"We literally spent hundreds of millions of dollars in Australia this year on extra hospital beds, extra doctors in emergency departments, the lost productivity of all the people staying home with sick children. We need to make sure that we don't buy the cheap one when their are better ones available because it's a false economy."

Prof Van Buynder also renewed calls for free flu vaccinations for children.

The department of health says Prof Murphy has been authorised to examine whether there are ways to strengthen the NIP, including discussions with manufacturers on new and strengthened vaccines.