The quarterly report released by the Australian Health Department analysed notification rates of diseases from January 1 to March 31.

Canberra had the highest rates of the vaccine-preventable disease pertussis, or whooping cough, with 124.8 cases per 100,0000 people which was double the national prevalence rate of 57.8 cases per 100,000 people.

ACT had 119 of the 3355 whooping cough cases reported nationally in the first three months of 2017.

Cases of whooping cough have risen year on year in the ACT, according to federal health department records.

In 2014 there were 233 cases in the ACT. That figure nearly doubled in 2015 with 487 cases that grew to 504 notifications of pertussis in 2016.

An ACT Health spokeswoman said pertussis was an unpredictable disease in terms of incidence and the past three years had significantly lower rates than the last large community-wide outbreak.

"During 2010 and 2011, there were 713 and 829 cases reported in each year respectively, which is significantly higher than more recent years," the spokeswoman said.

The whooping cough vaccine is provided free on the National Immunisation Program Schedule and data indicates pertussis vaccination coverage in the ACT is higher than most other jurisdictions.

In 2015 the ACT began offering free whooping cough vaccination to women in their third trimester of pregnancy to extend some protection to newborns too young for jabs.

Between 2014 and 2016 there were only seven cases of infants aged younger than six months with the disease.

To date in 2017, there has only been one case of pertussis reported in an infant younger than six months.

"ACT Health cannot definitively say why the rates of pertussis per 100,000 population are higher in the ACT compared to the national rate," the spokeswoman said of the latest figures.

The territory government has no plans to introduce another pertussis booster into the immunisation schedule, the spokeswoman confirmed.