Tchoungui was appointed Minister of Public Health when a new federal cabinet was announced on 20 October 1961. After federal legislative elections, on 1 July 1964 the cabinet was reshuffled. Tchoungui was appointed Minister of National Economy. In 1965 he was briefly Minister without portfolio. On 18 November 1965, East Cameroon Prime Minister
Vincent de Paul Ahanda was dismissed from office due to a dispute with President
Ahmadou Ahidjo. Tchoungui was named his successor, and would remain head of the East Cameroon government until May 1972. Ahidjo, who was from the
Hausa–Fulani north of the country, made a practice of appointing Beti Prime Ministers from the center/south to maintain balance. In June 1966 President Ahidjo called a conference that included the leaders of the two main political parties, the KNDP and CPNC and the prime ministers of West and East Cameroon. The participants decided to "reinforce national unity" by merging their parties into one, the
Cameroon National Union (In French:
Union Nationale Camerounaise - UNC). The new party came into legal existence on 1 September 1966, with Ahidjo as president and Tchoungui one of two vice-presidents. Elections were held for the Federal and East Cameroon governments on 7 June 1970 and were won by the UNC candidates, as expected. On 12 June 1970 Tchoungui was reappointed Prime Minister of Eastern Cameroun. He left this post on 20 May 1972 when the United Republic of Cameroon was declared. Tchoungui, a Catholic, played a role in the affair of Bishop
Albert Ndongmo. Ndongmo was credibly suspected of being involved with rebels led by
Ernest Ouandié. The Archbishop of Yaoundé,
Jean Zoa, requested that Tchoungui ask the Pope to summon Ndongmo to Rome and then invite him to remain there. Ndongmo, who insisted on his innocence, did go to Rome but then returned to face trial. He was arrested immediately after arriving, and after several months of interrogation faced a military tribunal in January 1971, which sentenced him to death for treason. Ahidjo later commuted the sentence to life imprisonment. The affair caused tension between Muslims and Christians: some churches were burned in the North. It also caused dissension among Catholics, some of whom condemned Archbishop Zoa for being too close to the government, and for possibly assisting in removal of a popular rival. ==Other activities==