In the aftermath of the 1966 Nigerian coup d'état, Aghanya was arrested on 18 January 1966 and together with Lieutenant Colonel Victor Banjo accused of plotting to assassinate the military head of state Major General Johnson Aguiyi-Ironsi. Aghanya was detained without trial at the Kirikiri Maximum Security Prison with others purportedly involved in the coup d'état. He was later transferred to Enugu and subsequently Abakaliki prisons. In retrospect, those actively involved in the planning and execution of the coup such as Major Adewale Ademoyega have attested to the innocence of both Aghanya and Banjo in their memoirs. After the 1966 Nigerian counter-coup in which Aguyi Ironsi was murdered, Aghanya was released from prison in March 1967 at the orders of the then governor of the Eastern Region, Colonel (later General) Odumegwu Ojukwu, defying the orders of new head of state Colonel (later General) Yakubu Gowon. In response Gowon announced the release of Aghanya and others after the fact.