Carter will visit the USS Theodore Roosevelt with Malaysian Defence Minister Hishammuddin Hussein, U.S. officials said.
The warship is "conducting routine operations while transiting” the East Vietnam Sea, Carter said on Wednesday after a meeting of defence ministers from Southeast Asia in Malaysia, a forum marred by U.S.-China disagreements over the busy sea lane.
China claims most of the East Vietnam Sea, through which more than US$5 trillion in global trade passes every year. Vietnam, Malaysia, Brunei, the Philippines and Taiwan have rival claims.
Carter's visit will come just a week after the USS Lassen, a guided-missile destroyer, challenged territorial limits around one of China's man-made islands in Vietnam’s Truong Sa (Spratly) archipelago with a so-called freedom-of-navigation patrol.
Beijing has rebuked Washington over the patrol while China's navy commander has warned that a minor incident could spark war in the East Sea if the United States did not stop its "provocative acts".
The U.S. Navy plans to conduct patrols within 12 nautical miles of artificial islands in the East Sea about twice a quarter to remind China and other countries about U.S. rights under international law, a U.S. defence official said on Monday.
U.S. defence officials have said Carter would not be on any warship carrying out such patrols.
"Teddy Roosevelt's presence there and our visit is a symbol of our commitment to our rebalance (to Asia) and the importance of the Asia-Pacific to the United States," Carter said on November 4.
In July, Admiral Scott Swift, commander of the U.S. Pacific Fleet, was on board a Boeing P-8 surveillance plane as it carried out a seven-hour flight over the East Sea.
Swift said his flight was routine, but it drew a stern rebuke from China, which said such activities seriously damaged trust between the two countries.
In May, Beijing called a P-8 surveillance flight carrying a CNN team over the East Sea "irresponsible and dangerous".
The 10-member Association of South East Asia Nations (ASEAN) scrapped a joint statement to be issued after their meeting on November 4 because they were unable to agree on whether it should refer to the East Vietnam Sea dispute or not.
The United States had lobbied for inclusion of a reference, while China had argued it had no place in the statement. Carter and his Chinese counterpart attended the meeting.
"The decision was made by ASEAN because there is no consensus, so no joint declaration is signed," Hishammuddin told a news conference.
U.S. Deputy National Security Adviser Ben Rhodes said Washington believed that the U.S. commitment to freedom of navigation was welcomed by ASEAN.
"People want the United States to be present, people want to know that the United States is going to be a stabilising force ... but they also want us to have a good relationship with China," said Rhodes, speaking at the Center for Strategic and International Studies in Washington.
The United States says it takes no position on the East Sea claims. China denies it's impeding freedom of navigation or overflight in the waterway.