"Australia should not count on being welcomed or accepted," if it is in airspace around the disputed territories, reads an editorial in the Chinese language version of the Global Times.
"The Chinese people cannot understand why the Australian military would get involved, and to be honest, they have less patience to prevent a flare up," according to the paper.
Beijing claims most of the South China Sea as territorial waters. However, Malaysia, Brunei, the Philippines, Vietnam and Taiwan have overlapping claims.
The BBC reported that it recently intercepted radio communications from an Australian aircraft flying within 12 nautical miles of the China-controlled islands. The pilots reportedly said they were carrying out a freedom of navigation (FON) flight.
The Australian Department of Defense said the flight was not an FON exercise, stating, rather, that it was a routine maritime surveillance patrol under Operation Gateway, launched in 1980 to preserve regional stability.
The Chinese newspaper editorial warned that "Australian military planes better not regularly come to the South China Sea to 'get involved,' and especially don't test China's patience by flying close to China's islands.
"Everyone has always been careful, but it would be a shame if one day a plane fell from the sky and it happened to be Australian."