More than 90 people have been admitted to Canberra hospitals and elderly patients have died as the H1N1 virus is replaced as the most prevalent form of influenza in the community.
The peak of the annual ACT flu season passed last month after a massive increase in laboratory-confirmed cases compared to the previous year.
Chief Health Officer Paul Kelly said that there had been 541 laboratory-confirmed cases of influenza up until August 24, compared with 193 during the same period last year.
The Canberra Hospital, Calvary Public Hospital and Calvary Private Hospital had admitted 94 patients with influenza, compared with just 18 in 2011.
Dr Kelly said H1N1, or swine flu, had been replaced as the predominant flu by the H3N2 virus.
''In 2010, 2011, it's been all HIN1, affecting mainly the middle-aged, whereas the typical flu season affects quite little kids and the elderly and can become quite severe for them for reasons not so much of the actual flu bug but because of their immune response capabilities,'' he said.
''In the previous years, with the H1N1, it was quite severe with those middle ages, because the flu bug was severe. Paradoxically, even though it's not a pandemic, we've seen more admissions and more emergency department presentations.
''It was really quite tough there for a few weeks.''
Some patients had been admitted to hospital intensive care units and a small number had died.
''We've had a couple of outbreaks in aged care facilities and not surprising some of those people had passed away,'' he said.
Dr Kelly said the increase in reported influenza cases could partly be the result of a change in testing practices.
''I think we've seen a lot more kids this year, which I think is partly due to that testing, but also partly due to the fact it's been a slightly different flu this year,'' he said.
Dr Kelly said the influenza vaccine had probably been slightly less effective this year than in previous years because it had vaccinated for a slightly different form of H3N2 than the one that had subsequently begun circulating in the community.
''It's a slightly different strain to the one that's been circulating, so it hasn't been as effective probably this year as it has in the last three years, just because it's slightly different one that's circulating,'' he said.
''The vaccine developed for next year would almost certainly include H3N2.''
The influenza season had peaked last month and only a small number of cases were now being reported. Queensland and Western Australia had also reported increases in flu cases this year, while rates had been more stable in other Australian jurisdictions.
Queensland was having a later flu season than the ACT, with the number of cases continuing to increase.
The ACT's flu season usually lasts for about six weeks but cases can occur at any time of the year.
Meanwhile, the number of pertussis or whooping cough cases has dramatically decreased across Australia.
Dr Kelly said 215 whooping cough cases had been notified in the ACT this year, down from 621 over the same period last year.
Nationally there had 15,020 cases, compared to almost 39,000 cases during all of 2011.
The drop was attributed to cyclical factors and an increase in vaccinations.
Whooping cough can be fatal in young babies.
The first scheduled vaccination for whooping cough has been brought forward from two months to six weeks of age.