Carter made the announcement while visiting the Philippines where American and Filipino troops are holding annual joint military drills.
Speaking at a news conference with Philippines Defense Minister Voltaire Gazmin Thursday, Carter said the two countries have been conducting joint patrols in the South China Sea and will increase them going forward to ensure security for the region's waters.
Carter also said U.S. aircraft will remain behind at Clark Air Base after the drills, and 200 airmen will continue joint training, conduct flight operations and lay the foundation for joint air patrols, to complement ongoing maritime patrols.
Carter also added that the United States and the Philippines have agreed to upgrade infrastructure at five locations in the Philippines. The U.S. has already released the first batch of money -- $42 million -- to support this program.
"This is a time of change in the region," Carter said. "We want to continue upholding stability and security in the region."
After the Philippines visit, Carter headed to the USS John C. Stennis currently crossing the South China Sea.
Pentagon spokesman Peter Cook tweeted out a video Friday showing the defense secretary's views as an F/A-18 plane landed on the U.S. aircraft carrier's deck.
This visit, which a U.S. official had told CNN about beforehand, is all part of Carter's extended trip to Asia and the Middle East.
Freedom of navigation
The Philippines and a number of other countries in Southeast Asia have territorial disputes with China over the South China Sea. China claims the whole of the South China Sea as its territory. China also has a territorial dispute with Japan over a set of islands in the East China Sea -- referred to by China as Diaoyu but called Senkaku by Japan.
"There's no question that there's concern in the region about China's behavior," Carter said. "The U.S. values peaceful resolving of disputes. The U.S. values freedom of navigation. Countries that don't stand for those things will be isolated. That is self-isolation, not isolation by us."
He added: "With respect to Chinese claims in the South China Sea and to all other parties, the American position is very clear, that these things should be settled peacefully and lawfully. We don't take sides in them per se. We are on the side of peaceful resolution."
Philippines Defense Minister Gazmin added the U.S. presence "will deter uncalled for actions by the Chinese."
China, meanwhile, accused the U.S. of taking a "lopsided approach favoring China's rival claimants."
In a commentary published by the state-run Xinhua news agency, Washington was accused of "going back on its words."
But it warned that "neither muscle-flexing nor arbitrary intervention will shake China's resolve to safeguard its sovereignty and maritime rights."
Then taking aim at Manila, the piece went on to state that "provocations, maneuvers, attempts to involve outsiders, or showing off a military alliance with Washington won't alter the historical fact of China's sovereignty over the South China Sea islands and adjacent waters."