The study, published in the British Journal of Sports Medicine, found that basketball players wearing this type of footwear were four times more likely to suffer ankle injuries.
These "air-filled" trainers have cells in their heels and soles to provide extra cushioning to the athlete.
The report's authors suggested that the air cells may make the foot less stable, increasing the risk of twists and sprains as the player jumps and turns.
And a British expert said that she had suspected the danger of air-filled trainers for some time.
The Australian team looked at a total of 10,393 "participations" in basketball, each representing one player taking part in a single match. The ankle injury rate was 3.85 per 1,000 of these participations.
No warm-up
More than half of those injured did not seek professional help for the injury. Failure to warm up properly before the game also appeared to increase the risk of injury.
Players who had had such injuries in the past were more than five times more likely to get injured. A separate Australian basketball study found that more than half the time missed by players was due to ankle injuries.
The authors wrote: "Further research is necessary to explore the hypothesis that air cells decrease rear-foot stability and consequently increase the risk of ankle injury."
Karen May, a chartered sports injury physiotherapist who has worked with the English Basketball Association, said that the finding supported her own suspicions about the trainers.
She said: "We've found that the air-filled sac can make the foot more unstable.
"When your foot lands in a strike position, and doesn't roll in the normal way, there is more risk of injury."
She said she suspected that not only air-filled trainers, but those with gel implants placed recreational athletes at greater risk.
"Many of the more fashionable trainers are unsuitable for some sporting activities, but people often don't know the difference."