U.S. officials said last week that the U.S. Navy avoided military drills that could have further inflamed tensions with Beijing.
The U.S.'s goal is to remind China and other countries about America's right to freely navigate the region.
The two officers held talks after a U.S. warship sailed within 12 nautical miles of one of Beijing's man-made islands.
The incident, although unusual, was characterized by the Pentagon as "safe."
U.S. Naval Destroyer Sailing Near Man-Made Islands in South China Sea Fuels Angry Rebuke From Beijing
A defense official said the mission would be the first freedom-of-navigation exercise to test China's territorial claims.
The patrols represent the most serious U.S. challenge yet to the territorial limit China claims around the islands.
Carter said on Tuesday that the United States military would sail and fly wherever international law allowed.
A senior U.S. official reportedly said U.S. ships would sail within 12-nautical-mile zones that China claims as territory.
Chinese President Xi Jinping began his weeklong U.S. visit this week.
Obama said the land reclamation projects are 'counterproductive.'
American interests are few and of middling importance.
U.S. Defense Secretary Ash Carter said the scale of Beijing's activities, not the United States, was altering the status quo in the region.
The Pentagon is considering sending military aircraft and ships to patrol the Spratly archipelago.
Tensions have festered over China's island building in the South China Sea.
The Chinese navy issued eight warnings to the U.S. P8-A Poseidon.
China could eventually deploy radar and missile systems on outposts it is building in the South China Sea.
"We are building shelters, aids for navigation, search and rescue as well as marine meteorological forecasting services."
Vice Admiral Joseph Mulloy told a congressional committee that China was building a large number of "fairly amazing submarines"
China and the U.S. are holding talks expected to focus on cyber-security, maritime disputes, the Chinese currency and an investment treaty
John Kerry pointed to China's introduction of an oil rig and several vessels in waters disputed with Vietnam as "provocative."
The United States has called China's deployment of an oil rig "provocative and unhelpful" to security in the region