From 1959 to 1960, Shagari was the pioneer Federal Minister for Economic Development of independent Nigeria where his Ministry was responsible for drawing the 1962–1968 development plan. Shagari's Ministry of Economic Development was also responsible for the establishment of the Niger-Delta Development Board. From 1960 to 1962, he the Federal Minister for Pensions which undertook the mission of Nigerianization of the civil service. From 1962 to 1965, Shagari was made the Federal Minister for Internal Affairs. From 1965 up until the first military coup in January 1966, Shagari was the Federal Minister for Works and had executed many important projects including Eko Bridge Lagos which was the first major contract of the German construction firm Julius Berger in Nigeria, and the completion of the Niger Bridge which was commissioned in 1966 by Prime Minister, Sir Abubakar Tafawa Balewa. In 1967 he was appointed as the secretary for Sokoto Province Education Development Fund. From 1968 to 1969, Shagari was given a state position in the North-Western State as Commissioner for Establishments.