Bataringaya was one of the first Ugandans to be detained by the new Idi Amin government. In the week after Idi Amin's coup d'état, Amin dismissed all of the ministers of Obote government but did not immediately imprison anybody except for Bataringaya. On 28 January 1971, three days after the coup d'état, Idi Amin brought fifty-five political prisoners imprisoned by the Apollo Milton Obote government to the Entebbe International Airport and freed them, while also bringing Bataringaya to the event in an army Jeep under armed guard, and was the only political prisoner not freed despite Amin's comment that "you need not fear for your safety since the new government is more interested in uniting Ugandans than anything else". Bataringaya was personally interrogated by Amin, where he likely revealed the other officers working to arrest Amin on 24 January 1971.