The Ministry of National Defense has dismissed an Australian media report claiming that the Chinese Navy challenged Australia in the South China Sea as "not in accordance with facts".

The Australian Broadcasting Corp cited anonymous defense officials in a report on Friday as saying that China "challenged" three Australian warships in the South China Sea, the Associated Press reported.

In response, the Chinese ministry confirmed in a Friday afternoon statement that naval vessels of China and Australia "had an encounter" on April 15 in the waters of the South China Sea.

The Chinese vessels used professional language in their contact with Australian naval forces, and their operations were legitimate, regulated, professional and safe, the ministry said without elaborating on the exact numbers of the naval vessels from either side.

"The relevant report made by Australian media is not in accordance with facts," the ministry said.

Also on Friday, Australian Prime Minister Malcolm Turnbull said the Australian navy has a "perfect right" to traverse the South China Sea, the AP reported.

When asked about Turnbull's comment, Foreign Ministry spokeswoman Hua Chunying said China always respects and safeguards the freedom of navigation and overflights enjoyed by all countries in the South China Sea in line with international laws.

If Australia has hidden intentions or indications in this regard, it is hoped the country would face up to the stable and good momentum in the South China Sea region's situation, work with China and other countries in the sea to maintain its peace and stability and inject positive energy into the region, Hua said.

A Beijing-based military expert with ties to the People's Liberation Army said Australia is only an outsider in the South China Sea region, and it should remain highly prudent and refrain from meddling.

It is natural to see Australia's hope to play a bigger role in the region, but the issue is whether it can play a positive, constructive role, said the expert, who asked not to be identified.