Fifteen hoax transmissions were reportedly made to aircraft over Melbourne, included one that forced a flight to abort its landing.
The illegal broadcasts were made over several weeks at Melbourne's main Tullamarine and Avalon airports, according to the Australian Federal Police.
Local media reported a portable radio may have been used to interfere with air traffic control.
The incidents did not pose a continuing threat to safety, the AFP said.
ABC News reported that a Virgin Australia aircraft changed altitude before aborting its landing after receiving instructions from a mystery person on October 27.
It also aired a recording of a conversation between an air traffic controller and a person pretending to be a light aircraft pilot giving a mayday call.
AFP head of crime operations Chris Sheehan said police were treating the security breach "extremely seriously".
"These incidents are being thoroughly investigated by the AFP, with technical support from the ACMA (Australian Communications and Media Authority)," he said.
"The airlines have been briefed to ensure the advice has been passed on to their pilots and to ensure appropriate measures are in place."
Making unauthorised transmissions on official air channels in Australia is punishable by up to 20 years in jail, according to the BBC.
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