A Chinese state-owned newspaper has issued a strongly worded warning to Australia about a Royal Australian Air Force (RAAF) surveillance plane carrying out "freedom of navigation" exercises over the South China Sea.

The editorial in the Chinese language edition of The Global Times appears to warn Australia its planes could be shot down if such operations continue.

Sorry, this audio has expired BBC audio: Australian pilot issues warning to Chinese Navy

On Tuesday, the BBC broadcast audio of an Australian pilot alerting the Chinese Navy of its flight over the disputed Spratly Islands.

"China Navy, China Navy," the voice said.

"We are an Australian aircraft exercising international freedom of navigation rights, in international airspace in accordance with the international civil aviation convention, and the United Nations Convention on the Law of the Sea."

The BBC said it recorded the message from a RAAF AP-3C Orion surveillance aircraft in the early afternoon on November 25.

According to the BBC, the message was repeated several times by the RAAF pilot, but no response was heard from the Chinese.

The Global Times editorial, which was toned down in the English language version of the newspaper, said: "Australia should not count on being welcomed or accepted" when it is in air space around the disputed territories.

"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," the newspaper said.

"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."

'Freedom of navigation in South China Sea out of question'

The newspaper goes further to say China and Australia are "friendly nations" and should have a "friendly relationship," suggesting diplomacy between the two nations could sour if Australia continues the flights.

"It's impossible to set up a military alliance against China in the South China Sea," the newspaper said.

"China has not violated the core interests of those countries, they come to the South China Sea to 'play cards', for other strategic goals, and they're not really there to oppose China."

On Tuesday, the Chinese Foreign Ministry voiced a more muted concern over the flight.

"The Chinese side has made its solemn position clear on many occasions," spokesman Hong Lei said.

"I'd like to reiterate that the freedom of navigation in the South China Sea is out of the question.

"Countries outside the region should respect other countries' sovereignty instead of creating trouble."

'It's what we do, it's called Operation Gateway': Payne

But Defence Minister Marise Payne said China should not be surprised about the flights.

"It's actually not an assertion of freedom of navigation, it's what we do, it's called Operation Gateway and it's been underway since 1980," Senator Payne said.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 4 minutes 5 seconds 4 m 5 s Defence Minister calls on media to explain aircraft broadcast Download 7.5 MB

"Perhaps the approach that the media take of a shock, horror revelation is one for them to take, not me."

Senator Payne argued such an operation was unlikely to provoke anger from the Chinese Government.

"I don't think the Chinese are at all surprised to know that Australia supports freedom of navigation, freedom of flight in accordance with the international law of the sea," Senator Payne said.

The Department of Defence in Canberra confirmed the flight took place between November 25 and December 4.

"A Royal Australian Air Force AP-3C Orion was conducting a routine maritime patrol in the region as part of Operation Gateway from November 25 to December 4," it said.

"Under Operation Gateway, the Australian Defence Force conducts routine maritime surveillance patrols in the North Indian Ocean and South China Sea as a part of Australia's enduring contribution to the preservation of regional security and stability in South East Asia."

China claims most of the South China Sea — where more than $5 trillion of world trade passes through each year — in the face of rival claims from Vietnam, Malaysia, Brunei, Philippines and Taiwan.