Jetstar flight JQ61 carrying 172 passengers from Darwin to Singapore was forced to turn around about half an hour after it took off from Darwin airport on Thursday night.
Jetstar spokesman Simon Westaway said it was believed the men had been drinking duty-free alcohol before they boarded the plane.
Despite being intoxicated, they passed several security checkpoints and boarded the plane.
Mr Westaway said the men became "disruptive" about 30 minutes after take-off, leaving the captain no option but to turn the plane around.
"We originally contemplated having security meet them in Singapore but the captain made the decision to go back to Darwin," he said.
Australian Federal Police officers were waiting at Darwin airport and escorted the five Malaysian men off the plane.
Two men were taken into protective custody. The other three were allowed to leave on their own.
The two men in custody were later released after Jetstar informed the AFP it did not want to pursue charges.
The disruption delayed the flight by about three hours.
"We are doing our own investigation as to how these individuals got on to the plane while intoxicated," Mr Westaway said. But he said Jetstar management supported the captain's decision to turn the plane around.
"Our captain and crew have a duty of care to all passengers," he said.