The AIS has treated a number of athletes because of Canberra's smoky haze that's equivalent to smoking a packet of cigarettes.
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AIS chief medical officer David Hughes released guidelines for athletes training in bushfire-affected regions on Thursday.
It comes after Canberra's been swamped by smoke blowing in from the bushfires raging in the region.
The Canberra Raiders and ACT Brumbies lead hundreds of elite athletes training in the rank air.
Cricket ACT cancelled Saturday's games, Netball ACT have cancelled social competitions during the week and Canberra United canned their fan day on Friday.
Hughes said the unprecedented number of bushfires had forced their hand with athletes affected by the conditions around the country.
According to AIS guidelines, anything above 150 on the air quality index is "hazardous" and all outdoor training should be moved indoors.
The AQI peaked at 983 in Florey at 10am on Friday - more than six times the hazardous threshold.
Hughes said asthmatics were most at risk of suffering effects from the smoke, but they'd treated a number of athletes who were feeling the after effects.
He said athletes shouldn't be "unnecessarily alarmed", especially given what the firefighters are dealing with.
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But he said coaches and fitness staff should check the AQI each day before training.
For smoky air the AQI measures the amount of fine particles, known as PM2.5, present. They're invisible to the human eye.
At low levels the lungs are able to clean them out, but at high levels they struggle.
"If this lasts for several weeks and then clears, there's no evidence of long-term harm - people are likely to just get on with their normal lives and be completely unaffected," Hughes said.
"They'll develop things like itchy eyes and itchy nose, and perhaps a sense of irritation in their lungs.
"We've had athletes presenting here at the AIS with the effects of smoke inhalation ... and we've had large numbers of athletes here at the AIS training indoors over the past week or two.
"Where we've had readings of up over 700 micrograms that can be the equivalent - if someone was breathing in large volumes of that air - of smoking a packet of cigarettes."
Hughes said some athletes were more at risk than others.
Those doing high-intensity aerobic training for long periods, like rowers and cyclists, were more susceptible.
But those doing short bursts of power training would be less so.
"There's a huge difference between someone say training to throw a javelin, where they're doing short bursts of high-intensity work -that's not very aerobic - against someone that's doing highly aerobic sports like rowing on a lake at high intensity, or cycling at high intensity, for prolonged periods of time - maybe up to one or two hours at a time in one training session," Hughes said.
"They're breathing in huge amounts of air and if the air is polluted they're therefore breathing in huge amounts of that particulate matter.
"But people doing short bursts of anaerobic activity are not necessarily at much greater risk than someone walking around in the general population."
Canberra tennis player Alison Bai's training has been affected, with the Canberra Tennis Centre closed due to the smoke on Wednesday.
She felt it was similar to playing in China, where pollution is a problem, but the current smoke was a bit harsher.
"[Wednesday] we had to cut our training short because the air pollution wasn't good. I could feel it in my lungs already," Bai said.
"They closed the tennis centre in Lyneham. It was okay but one of the guys said, 'You know how you play overseas when the air pollution is so bad.'
"But I said, 'If you can play in China you can play anywhere', the air pollution is so bad there.
"But it's a different kind of air pollution. I feel like I've smoked a pack of cigarettes.
"In China it's more industrial pollution, so you don't feel as scrappy in the lungs."
Raiders recruit Matt Frawley said they'd been doing their running in the morning to avoid the worst of it.
The smoke has been rolling into Canberra in the evenings on the sea breeze.
"It's something all the clubs are dealing with in Sydney and down here it's no different," Frawley said.
"We try to get our running done in the morning before it gets too bad. It's just something we've got to deal with I suppose."