CT scans are used by doctors to get to the core of a problem by creating a 3D image of the most inaccessible nooks of the body.
But the beams of ionising radiation can cause cellular damage.
A fresh analysis of 2013 research is being presented by researchers from the University of Melbourne at the World Congress of Public Health in Melbourne.
They said the radiation risk was much greater than previously acknowledged.
The results indicated that most of the excess cancers occurring more than two years after a CT scan were caused by radiation from the scan.
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John Mathews and his team from the University of Melbourne examined the Medicare and cancer records of almost 11 million Australians aged up to 19 years old.
"The risk is increased to a small extent, possibly one extra cancer for every 2,000 exposed to a CT scan," Professor Matthews said.
The study found that more than 3,100 children who had been given a CT scan had developed cancer — 24 per cent higher than children who had not had the scan.
The researchers found that the risk of developing cancer increased by 16 per cent for each additional CT scan.
"What we found was that the younger people were at the time of the CT scan, the greater the increase in relative risk," Professor Mathews said.
"Whereas if they were exposed as adolescents, then the relative increase in risk was smaller.
"The absolute risk does tend to go up with increasing age at diagnosis."
Professor Mathews said his team suspected this had something to do with the way cells "turn over" in younger people.
"They do seem to be more sensitive to the insult from the ionising radiation that can eventually lead to cancer," he said.
Doses 'lower now as a rule'
Michael Ditchfield, president of the Australian and New Zealand Society of Paediatric Radiology, admitted that it was difficult to find the right balance when deciding whether to use a CT scan on children.
"In a child that's come in [to hospital] with major abdominal trauma, where the child will die unless appropriately assessed, [it's] definitely worth the risk," Professor Ditchfield said.
He said CT scanners had improved dramatically in recent years.
"[CT scanners are] considerably more sensitive, to the point that the doses used may be 100-fold less," Professor Ditchfield said.
"The techniques used for some areas such as the chest — we know we can use much lower doses.
"So it's important data … but it's important to be aware that the doses we use now are lower as a rule."
Bastian Seidel, president of the Royal Australian College of General Practitioners, said GPs generally tried to avoid using radiation when investigating injuries in younger children.
"But sometimes it's just necessary," he said.
"For example, if your child has a severe head injury caused by an accident, it might just be necessary to undergo a CT scan to make sure there's no damage to the brain, no damage to the skull.
"So we don't use CT scans very often, but sometimes we just have to."
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