Mr Austin spoke by phone with Philippine Secretary of National Defense Delfin Lorenzana while he was flying from Washington to Israel to begin an international trip.
Pentagon press secretary John Kirby said Mr Austin and Mr Lorenzana discussed the situation in the South China Sea and the recent massing of Chinese vessels at Whitsun Reef, which has drawn criticism from Manila.
In their phone call, Mr Austin proposed to Mr Lorenzana several measures to deepen defence cooperation, including by “enhancing situational awareness of threats in the South China Sea,” Mr Kirby said.
Mr Kirby said earlier this week that the aircraft carrier USS Theodore Roosevelt and its strike group, as well as the amphibious ship USS Makin Island, are operating in the South China Sea.
The recent gathering of Chinese vessels near the Philippines is among moves the United States has criticised as efforts by Beijing to intimidate smaller nations in the region.