[1] In March 1959, when Sir Robert Armitage, the Governor declared a State of Emergency, Bwanausi was arrested as a leading Congress member and detained without trial until 1960.
On his release, he returned to teaching, but joined the Malawi Congress Party and in 1961 was elected to the Legislative Council, becoming Minister of Internal Affairs and Development in the same year.
Banda's failure to consult other ministers, keeping power in his own hands, maintaining diplomatic relations with South Africa and Portugal and a number of domestic austerity measures caused two confrontations in cabinet meetings, which Bwanausi attended.
[4][5] Banda decided not to agree to the ministers' demands, and on 1 September, he advised the Governor-General of his intention re-form the cabinet replacing a number of them by his close followers.
[6][7] Despite attempts by the Governor-General to mediate, and Banda's willingness to re-instate Bwanausi, his colleague, Willie Chokani and possibly one other minister, the ex-ministers' insistence on all of them being reinstated and outbreaks of violence later in September 1964 ended any hope of a reconciliation.
[8] Bwanausi and Chokani resumed teaching in Zambia, where they, and were active in Malawian exile politics becoming a prominent member of the Pan-African Democratic Party which had been formed by another ex-minister, Henry Chipembere.