SEOUL, South Korea — The Trump administration has reaffirmed that the United States will pay for a missile defense battery it is deploying in South Korea, despite President Trump’s recent statement that he wanted Seoul to cover the cost, officials here said Sunday.

Mr. Trump caused alarm here on Thursday when he told Reuters that he wanted South Korea to pay for the Terminal High Altitude Area Defense system, known as Thaad, which is being installed as a defense against North Korean missiles. According to South Korea, the two allies had agreed that the Americans would pay for the system and its operation and maintenance, with Seoul providing land and supporting infrastructure.

On Sunday, the White House national security adviser, Lt. Gen. H. R. McMaster, called his South Korean counterpart, Kim Kwan-jin, and “the two reconfirmed what has already been agreed” about the system’s costs, Mr. Kim’s office said in a statement.

General McMaster “explained that the recent statements by President Trump were made in a general context in line with the U.S. public expectations on burden sharing with allies,” Mr. Kim’s office said.