In 1957, Muortat was denied a transfer to the Southern Sudan, so he resigned his position and joined the Sudan Civil Administration. He was appointed assistant district commissioner and served in many places in the Bahr el-Ghazal and Upper Nile provinces. In 1965, under the transitional government of Prime Minister Sirr Al-Khatim Al-Khalifa, Muortat was appointed to be Minister of Works and Mineral Resources in his cabinet.