He returned to Nyasaland in 1957, and founded and became first headmaster of the secondary school of the Henry Henderson Institute, a part of the Blantyre Mission which had previously only offered primary and vocational education.
In March 1959, when Sir Robert Armitage, the Governor declared a State of emergency, Chokani was arrested as a leading Congress member and detained without trial until 1960.
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 Chokani attended.
[5] In the first, on 10 August 1964, all the ministers present asked Banda to stop making slighting references to them in speeches and not to hold so many government portfolios himself.
[6][7] 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.
[8][9] The Governor-General attempted to mediate, and Banda's was willing to re-instate Chokani and one or two others, but the ministers' insistence that they should all be reinstated led to a failure of these initiatives.
During his enforced absence from Malawi, Chokani remained politically active and later moved to Tanzania as the treasurer of the Pan-African Democratic Party formed by another ex-minister, Henry Chipembere among Malawian exiles.