The Ministry of National Defense has dismissed an Australian media report claiming 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 "made an encounter" earlier this month in the waters of the South China Sea.

The Chinese vessels used professional language in liaison with the Australian side, 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 Australia 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, 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 could 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.