Malek served in the Nixon administration in several different roles, including Deputy Under Secretary of Department of Health, Education, and Welfare under Secretary Robert Finch, as special assistant from 1970–73 and deputy director of Nixon's re-election campaign. Malek served as deputy chief of the Committee to Re-elect the President in 1972.

As an efficiency expert to Nixon, Malek helped restructure Nixon's staff and officials and streamline the bureaucracy. In his memoirs, Nixon described Malek as a "tough young businessman whose specialty was organization and management."

In the first Nixon administration, Malek designed and directed the "Responsiveness Program", a strategy to replace civil servants with Nixon supporters and to steer government resources to benefit Nixon's 1972 re-election. According to the Senate Watergate report, Malek wrote in a 1972 memo to Haldeman that someone was needed to "take the lead in the program to politicize Departments and Agencies" and to "supervise the patronage operation and closely monitor the grantmanship operation." In advocating the plan, Malek wrote of "substantial risks" to politicizing the Executive Branch and expressed concern that the plan would "undoubtably backfire" if made public; therefore he recommended that "to minimize any links to the President, there should be no directions on this project in writing."

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In 1971, Richard Nixon became convinced the Bureau of Labor Statistics (BLS) had come under the control of Democratic rivals and what Nixon termed a "Jewish cabal." He instructed aides Charles Colson and H. R. Haldeman to identify a list of Democrats and "important Jewish officials" at the agency. Malek provided the data on Democrats after a check of voter registration rolls, but balked at fulfilling the rest of Nixon's query. "I refused four times. The fifth time he came back and gave me a direct order through Haldeman, so I gave him a number. I regret my compliance. It was a mistake." Malek did not have access to BLS employees' religious affiliations, so his list comprised those BLS employees with "Jewish-sounding names", and two months after he sent the list, two of the officials on it were reassigned to "less visible jobs" within the Labor Dept. Slate columnist Timothy Noah, however, asserts that a September 8, 1971 memo from Malek to Haldeman appears to contradict Malek's assertions of limited involvement, in which Malek states he has recommended to the Secretary of Labor "fairly drastic moves" including the "compromise" reassignment of three officials. Documents released by the Nixon library in January 2010 also appear to contradict Malek's statement.