But the opposition says it shows the ACT's health system is in "crisis mode".

Responding a question on notice from opposition health spokeswoman Vicki Dunne, Ms Fitzharris said Canberra Hospital was at alert level three throughout July, August and September last year.

That is compared to 2016 when there were just five equivalent code yellows during the same period.

Alert level three - formally known as code yellow - is an emergency response to deal with an internal incident that threatens the flow of critical services to patients.

It is triggered when two or more events relating to bed occupancy or service capacity occur.

The health minister could not immediately identify which triggers led to the alerts throughout the three month period.

A spokeswoman said it could have been any one or a combination of any of those events, on any given day during that period.

The Canberra Times reported in August the emergency departments were "standing room only" and corridors were "lined with beds".

"As you can appreciate, last year was a particularly bad flu season .. the ACT was not immune," Ms Fitzharris said.

"We saw hospitals across the country struggling to keep up with the significant impact of a particularly ... bad flu season.

"We have a very good plan in place not only to deal with this upcoming flu season but to deal with the upcoming needs of the people in the territory."

Ms Fitzharris said a number of measures were put in place during to period to safely manage capacity.

This included additional nurses recruited in paediatrics, adjusted ward rosters, more hospital assistants and improved communication strategies.

Asked whether Canberra Hospital was equipped to deal with crises, Ms Fitzharris said there had been increased collaboration between Canberra and Calvary hospitals.

She said the opening of Canberra rehabilitation hospital in July would ease pressure off main general hospitals.

But Mrs Dunne said the government should have planned for potential bad flu outbreaks.

"We have a flu season every year, this is a foreseeable event that the government should know to plan for," she said.

"While last year was worse than most the other sick people in Canberra shouldn't have to be put on hold because of the government's poor planning."

Mrs Dunne said Ms Fitzharris should confirm exactly how many, and which criteria triggered the alert level threes.

"This is an alarming revelation," she said.

"Minister Fitzharris keeps assuring Canberrans that our health system is in good form when the naked truth is; our health system is in crisis mode.

"We have missing and manipulated health data, we have long and painful waiting times, we have overflowing emergency departments, and we have high risk critical infrastructure.

"The government's irresponsible handling of our hospitals is compromising patient safety.

"She should deliver a comprehensive and actionable strategy to prevent this from happening again."

Triggers for alert level three: