Some northside residents are facing waiting lists of up to six weeks for vaccination appointments at maternal and child health immunisation services.
The delays come as influenza experts warn that Canberrans have only six weeks to be vaccinated against influenza with the government-funded shot delayed after modifications.
An ACT Health spokeswoman said maternal and child health services were undertaking "a number of strategies to address the current waiting time on the northside".
"The current wait time in south Canberra is under a week and there are a number of other locations across Canberra," she said in response to a complaint on social media.
The northside nursing services can be accessed in Belconnen, Dickson, Florey, Gungahlin, Ngunnawal and West Belconnen.
Influenza cases are known to increase in June and peak in August, which leaves little more than a month before the beginning of the flu season.
"The maternal and child health immunisation service is well attended and this has led to longer waits for appointments in the north side of Canberra [four weeks], Gungahlin [six weeks] compared to just under a week on the south side," the spokeswoman said.
"Parents should plan their children's appointments well in advance and keep these appointments. especially for the whooping cough vaccine, as children need to keep up with their scheduled vaccine dates."
On Monday, the government-funded influenza vaccine was made available under the National Immunisation Program after a rare change to protect Australians against a drift in the virus.
The southern hemisphere vaccine now contains the H3N2 strain which led to a severe influenza season in the northern hemisphere and the late outbreak of influenza B in Europe.
Health Minister Sussan Ley said the change to the vaccine was consistent with international and national advice and would ensure Australians received the most appropriate protection.
"The message is simple – get your flu shot before the flu gets you this winter," she said.
"The more people who are vaccinated, the less chance the illness spreads throughout the rest of the community. This is particularly true for those Australians who are ill, vulnerable, pregnant or elderly."
The ACT Health spokeswoman encouraged everyone in the community to be vaccinated to ensure immunity from diseases such as whooping cough and influenza.
"The best defence against any disease is prevention, vaccination is the best form of prevention," she said.
Under the National Immunisation Program the flu vaccine is free for pregnant women, people aged over 65, Aboriginal and Torres Strait Islander people aged over 15, and anyone at serious risk of influenza.
Dr Paul Van Buynder, a director of the Influenza Specialist Group, said last year's influenza season was the worst Australia had seen and action needed to be taken by authorities.
"We are concerned because last year we had the worst influenza season Australia has ever seen," he said.
"After that we saw that the influenza vaccine in North America was not a good match for a drift in the virus, which resulted in a very bad season."
There were almost 68,000 confirmed cases of influenza throughout Australia last year compared to 28,312 in 2013 and 59,027 in 2009.
Dr Van Buynder said there were already more influenza cases recorded this year compared to this point of time in 2014.