On 3 October he was arrested by the government as part of a wave of detentions meant to target alleged accomplices of the rebel group Rwanda Patriotic Front (RPF).
The vice-rector of the National University reinstated him on 9 April, but asked him to "adapt to the arrangements made in his absence", which meant he was deprived of all administrative responsibilities.
[2] The vice-rector and the dean subjected Habyalimana to harassment thereafter, attempting to oust him from his position in the applied sciences faculty and denying him backpay for his time in detention, even though the latter was in contradiction of instructions given by the rector.
President Juvénal Habyarimana of the ruling National Revolutionary Movement for Development (MRND) was wary of the effect this would have in Butare Prefecture, as it would mean a "strong" prefect from the Social Democratic Party (PSD) then working in Gitarama would assume the office.
Habyarimana concluded that a new, relatively non-political Tutsi should be appointed to the office, believing this type of person would make for a politically impotent prefect.
Habyalimana was viewed favorably by the government as a skilled academic who cared little for ethnic and regional differences and could collaborate with Hutus and northerners.
[2] During Habyalimana's two-year tenure as prefect, Butare experienced increasing political disorder as municipal officials were purged and murdered.
[10][11] Two days later the Hutu propagandist broadcaster Radio Télévision Libre des Mille Collines (RTLM) declared that Tutsis were concealing themselves amongst displaced persons fleeing to Butare Prefecture.
[13] The International Criminal Tribunal for Rwanda later ruled that this was done by the interim government since it concluded that Habyalimana would resist its desire to incite massacres of Tutsis.
[3] Habyalimana was present at the inauguration of the new prefect, Sylvain Nsabimana, on the morning of 19 April in Butare town,[13][15] but fearing for his personal safety he soon went into hiding.