Before entering the UN, Sanjuan was the first Assistant Secretary of the Interior for Territorial and International Affairs to be confirmed by the U.S. Senate. In that capacity, he formulated and administered United States policy toward the U.S. flag territories and the Trust Territory of the Pacific Islands. He was known jokingly as "the Viceroy of the Pacific." As Assistant Secretary of Interior, Sanjuan fought for strong financial support for U.S. territories against the tendency of the Office of Management and Budget to cut all entitlement programs. He also became identified with the urgent need to end corruption as a way of life in the administration of U.S. territories. In addition, he was the Interior Department's focal point for analysis, development, and review of policies and programs pertaining to all Interior Department international activities, which included managing the Azir National Park in Saudi Arabia, dealing with acid rain problems with Canada, clean water issues with Mexico and mining agreements with the Federal Republic of Germany. He also represented the department in Law of the Sea negotiations. At Interior, Sanjuan developed and managed a $250 million program and served as an advisor to the Presidential Personnel Office in the White House. He also co-chaired a White House task force on territories. He organized a plebiscite in Micronesia that led to the creation of three new countries now represented at the United Nations.

While Assistant Secretary of Interior, Sanjuan established the Micronesian Bureau of Investigation with the help of the FBI to prevent drug trafficking in the South Pacific.  He was made the MBI's Honorary Chief, and later appointed a major in the Guam police and a captain in the Virgin Islands police.

Before joining Interior, Sanjuan was founder of the American Enterprise Institute's Hemispheric Center and was its first director. He joined the Institute as a resident fellow in 1978 in charge of nuclear proliferation issues. Sanjuan served as Director for Public Affairs of the Arms Control and Disarmament Agency from 1975 to 1977 and spent the better part of 1977 on the Carter White House staff working on arms control issues at the request of Zbigniew Brzezinski and Hamilton Jordan and assisted in the passage of the Panama Canal Treaty legislation through Congress. In 1976, just after being detailed to Carter’s White House staff, Sanjuan was selected as the White House representative to accompany the chairman of the Senate Foreign Relations Committee, Frank Church, on a ten-day trip to Cuba as Fidel Castro’s guest.

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