In the aftermath of the December 1965 elections, there was a bloody military coup on 15 January 1966, establishing a National Military Government. Olowofoyeku was arrested and taken into custody by the Military Government on 30 January 1966 and detained for six months. He was first detained at Agodi in Ibadan and later transferred to KiriKiri in Lagos. He was allowed very limited family visitation rights throughout his political incarceration at KiriKiri.