Western Australia's justice department said three teenage detainees were aboard the charter flight from Broome in the state's north on Wednesday.
The incident is alleged to have happened just minutes into the flight before youth custodial officers intervened.
"As the officers moved to bring the detainee under control, he started kicking the plane's interior and the two other detainees joined in the disturbance," the department said in a statement.
"The three detainees, all aged 17, were quickly brought under control."
The department said the detainees had been in restraints in accordance with security protocols and there were no injuries or damage to the plane.
The plane was redirected safely back to Broome Airport.
Police took the teenager they described as the "principal offender", who was allegedly involved in a police pursuit incident in Broome earlier this week, into custody at the airport.
Officials said a second charter flight and additional staff would be arranged to transport the boy, while the two others were flown to Perth later on Wednesday.
Premier Mark McGowan described the incident as "very disturbing".
"Can I pass on my thoughts and thanks to the staff and the pilots on that aircraft for the way they managed that very, very difficult situation," he told reporters.
"This sort of extreme behaviour is what we're dealing with and it's completely and utterly unacceptable ... I'm just glad there wasn't a tragedy out of it."
Mr McGowan indicated additional safeguards would be provided for the alleged offender's transfer.
"The sorts of restraints that will be put in place will be what's necessary to deal with someone who acts like that," he said.
Youth detainees in WA are housed at the Banksia Hill detention centre in Perth.
An independent inspector this year found some boys at Banksia Hill were spending as little as one hour a day outside their cells, in violation of their human rights.
The McGowan government has promised to open an on-country detention centre in the Kimberley, where youth crime has been a major issue in recent years.
Mr McGowan on Wednesday said extensive consultation was required but the centre would be opened as quickly as possible.
"That won't mean every young person convicted of an offence will go to that facility," he said.
"It's designed to ensure as many people can stay on country as possible but some of these behaviours just mean you'll have to go to Banksia Hill."
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