The ambulance, from the nearby Dickson ambulance station, has been using the fire station as its temporary post since the Dickson site flooded during heavy rains on Saturday.

But firefighters union secretary Greg McConville says the ageing, heritage-listed station has ongoing problems with safety, and is not the place for a vehicle used to carry patients.

"We've got a dispute over the safety of the facilities in the first place, and the dispute concerns are the need for a separation between clean and dirty traffic areas," he told Fairfax Media.

"The design templates for pretty much all fire stations in Australia now create that separation, because when a firefighter comes back from a job, their clothes are impregnated with carcinogens, and these are very fine particles in smoke," he said.

"Of course, as you go back to the station and you remove that gear from the truck, it's all contaminated, so you get contamination of the engine bay. And we say it's not a suitable place for a patient transport vehicle to be stationed in the short to medium term, let alone long term."

Mr McConville said following the weekend's flooding, the firefighting staff were only too happy to help out their Dickson emergency comrades as a stopgap while water was cleared up.

But they've now been told that the ambulance might be stationed there for up to a month, and would depend on arrangements to be made with the Transport Workers Union.

"I really don't see that it should be up to the unions to make arrangements ourselves for the safety of our members, or the public for that matter," he said.

"We were never approached by the employer. In the first instance, it was the representative bodies coming up with a solution to a problem, and it was intended to stop the ambulance drivers and paramedics from having to quite literally park the ambulance by the side of the road and wait there pending a job - they had nowhere else to go."

But a spokeswoman for the ACT Emergency Services Agency Commissioner said there were no concerns about the safety of the Ainslie fire station.

"It is currently a fully operational station with no evidence of contamination," she said.

"The handling of exhaust fumes from fire trucks means that the air quality within the station is well above the limits set by Australian workplace exposure standards."

She also confirmed that the ambulance would remain at the Ainslie station while "remediation work" was carried out in Dickson to repair damage from storm water.

"This work is expected to be completed within the coming weeks. The relocation of the ambulance crew, which has been in place since Tuesday evening, will ensure that ambulance response times are minimised for the community in that part of Canberra."

Mr McConville said he was concerned also that planned upgrades for the fire station would be futile, given the building's heritage status.

"There is a proposal to renovate the fire station to take in additional crew, and we're saying well hang on, we don't know to what standard, and you haven't addressed our concerns about these particular [contamination] issues, and so pending that, we don't want you to change anything - we don't want you to waste your money."