China and the United States should manage their differences over disputed waters in the South China Sea constructively, one of China's top military officials has said.

Fang Fenghui, a member of China's Central Military Commission, told General Joseph Dunford, chairman of the Joint Chiefs of Staff, the two sides should "refrain from actions detrimental to the relations between the two countries and the two militaries", state news agency Xinhua reported on Friday.

Fang and Dunford discussed the South China Sea in a video link-up on Thursday, it said.

The discussion comes at a time of heightened tension between China and the United States, which have traded accusations of militarizing the South China Sea as China implements large-scale land reclamation and construction on disputed features while the United States has increased its patrols and exercises.

On Tuesday, China scrambled fighter jets as a U.S. navy guided missile destroyer sailed close to a disputed reef in the South China Sea and denounced the patrol as an illegal threat to peace.

The U.S. defense department said the latest "freedom of navigation" operation was undertaken to "challenge excessive maritime claims" by China, Taiwan, and Vietnam that were seeking to restrict navigation rights in the South China Sea.

China claims most of the South China Sea, through which $5 trillion in ship-borne trade passes every year. The Philippines, Vietnam, Malaysia, Taiwan and Brunei have overlapping claims.

Fang said China was not to blame for tensions with the United States in the South China Sea and urged the two sides "to bear the overall situation in mind and manage their differences in a constructive way", Xinhua reported early on Friday.

Xinhua quoted Dunford as calling for restraint in the South China Sea, and saying the United States was willing to work with China to establish "an effective mechanism on risk control so as to maintain stability in the South China Sea by peaceful means".

The South China Sea was also discussed at a separate meeting between Sun Jianguo, an admiral and deputy chief of the General Staff of the People's Liberation Army, and Vice Admiral Ray Griggs, vice chief of the Australian Defence Force.

Australian Prime Minister Malcolm Turnbull backed the United States on Thursday in its latest South China Sea patrol. Australia has consistently supported U.S.-led freedom of navigation activities there.

China's Defence Ministry said Sun told Griggs the South China Sea was not and should not become an issue between China and Australia, and that Australia should not do anything that "harms regional peace and stability or Sino-Australia ties".