Thomas K. Latimer, a longtime intelligence official in the Defense Department and the Central Intelligence Agency, has been chosen staff director of the new House committee created to oversee the nation's spying operations.

Latimer, 44, is deputy assistant secretary of defense for programs and resources in a Pentagon office dealing with communications and intelligence. His title from January, 1976, until last month, when the office was reorganized, was principal deputy assistant secretary of defense for intelligence.

Latimer is considered a protege of James R. Schlesinger Jr., now Secretary of Energy, when he was CIA director in 1973 and Defense Secretary from August, 1973, to November, 1975.

At the CIA, Latimer was Schlesinger's executive assistant and at Defense he was deputy director of the net assessment office, which keeps tabs on weapons systems of foreign countries. Ultimately he became Schlesinger's deputy secretary of defense. Schlesinger, a Nixon appointee, was fired as defense chief by then-President Ford, who said he wanted his "own team."

Latimer is expected to take the $47,500-a-year directorship of the House Intelligence Committee in the next few weeks. The committee, a counterpart to the Senate Intelligence Committee, will oversee the CIA and the rest of the intelligence community and will have control over the intelligence budget.

Last week the House approved a $302.499 budget for the new committee for the rest of the year. Its chairman is Edward P. Boland (D-Mass.). The chief counsel will be Michael J. O'Neil, 30, who has been legislative assistant to Boland for the last four years. O'Neil will be paid $45,000.

Latimer, who holds a doctorate in history from Georgetown University, was an intelligence analyst at the CIA from 1958 to 1967. He held a congressional fellowship the following year and in 1969 and 1970 headed the China branch in the current intelligence office at the agency. From 1970 to 1973 he was staff assistant to Henry A. Kissinger, then national security affairs adviser to President Nixon.