Scans later revealed two fractured ribs and a pneumothorax - a pocket of air between the ribs and lungs.
The injury creates pressure on the lungs and makes breathing difficult.
"Courtney will remain in hospital for a couple of days to receive treatment," HRT said in a statement.
The Department of Defence said the helicopter was participating in an "authorised and routine display" as part of the popular series.
The Royal Australian Navy and V8 Supercars have both launched investigations into the incident.
Co-driver Jack Perkins took Courtney's place in the No.22 Commodore for the day's final session, and will do so the rest of the weekend.
Courtney earlier tweeted a photo of himself in the back of the ambulance wearing an oxygen mask and wires attached to his chest.
"Didn't think this was going to happen today ... Doc has me flying," the 35-year-old posted.
Missing the round's three sprint races - the last before the endurance series - effectively ends Courtney's hopes of a second title.
He currently sits fifth on the championship standings, 371 points behind Ford's leader Mark Winterbottom.
The Sydney-born driver has had one victory and four other podiums so far this season.
It's not the first time Courtney has suffered serious injuries in V8 Supercars.
In November 2013, he fractured his tibia and tore his right quadricep after a horror crash during the opening race of the event at Phillip Island.
Chief executive James Warburton later announced V8 Supercars would cancel plans for further helicopters over the weekend as a result of the accident.
"Our thoughts are with James and we wish him a speedy and full recovery," he said in a statement.
- AAP
