The agency “has identified items marked as classified national security information within the boxes,” according to a letter posted on the National Archives and Record Administration website that was sent to Representative Carolyn B. Maloney, Democrat of New York and the chairwoman of the House Oversight Committee, who has been scrutinizing how Mr. Trump handled presidential records.

“Because NARA identified classified information in the boxes, NARA staff has been in communication with the Department of Justice,” said the letter, written by David S. Ferriero, the national archivist.