Khan was kept under house arrest at his Abbottabad residence from 16 October 1979 to 2 October 1984 and was named a prisoner of conscience by Amnesty International. In 1986, Khan left the MRD, which was under the influence of the Pakistan Peoples Party (PPP) and Awami National Party (ANP), and had paving a way for the Bhuttoism which had irked Khan. His decision of boycotting the non-partisan 1985 Pakistani general election eventually led to many of his party's key member defecting to the Pakistan Muslim League led by its President M. K. Junejo.