The company said flight MH128 flying from the Australian city to Kuala Lumpur was forced to turn back because of a "disruptive passenger".
"Following the incident on MH128, the disruptive passenger has been apprehended by airport security".
The statement gave no other details of the incident.
The airline has offered affected passengers accommodation at hotels and tickets on the next available flights or on other carriers.
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It said MH128 landed after being airborne for 14 minutes. He was eventually subdued by airport security and authorities said "a safety plan was enacted".
The passengers helped the flight crew restrain the passenger, a Sri Lankan national who was apparently drunk.
Malaysia Airlines stressed that "at no point was the aircraft "hijacked". "The man did not gain entry to the cockpit".
The flight returned to Melbourne's Tullamarine Airport less than an hour into the flight.
"The plane landed safely at the airport and passengers are now exiting the plane and speaking to investigators".
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Tullamarine Airport officials did not immediately respond to requests for comment.
Malaysian Airlines has suffered a number of high-profile incidents over he past three years, with the disappearance of MH370 in 2014 resulting in the presumed deaths of 239 people on board and prompting an worldwide search for the never-recovered plane.
In a few months after MH370 went missing, Flight MH17 from Amsterdam to Kuala Lumpur was shot down in eastern Ukraine.
She said her boyfriend, who is yet to be identified, had asked her "call everyone" because passengers could see police on the tarmac but that there was "no people coming in to get them".
Callers to the station also reported seeing passengers exit the aircraft about 1.30am (Melbourne time).
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