Nsengimana, 54, was head of College of Christ the King of Nyanza, southern Rwanda, one of the most prestigious schools in Rwanda.
The priest is charged for genocide and crimes against humanity committed in Nyanza and its surroundings. He has pleaded not guilty. His trial started in June 2007.
The protected witness known only as "BVX" alleged that Nsengimana was the leader of a death squad which killed several Tutsis around the college.
According to the witness, who lost her husband during the genocide, the deadly squadron was mostly composed of employees of the college.
The witness alleged that the priest never recruited Tutsis into the college.
"Hormisdas never hired Tutsis. There were only Hutus that worked at the college... When the genocide started, the Hutus took part in the killings", claimed the witness.
According to her, the alleged squad killed several people around the college, in particular on
3 May 1994. "I was able to observe the victims being killed with hoes", she added.
Mrs BVX added that women were raped before being killed. "They systematically raped the women before killing them", she told the court.
One of Nsengimana's lawyers, David Hooper indicated that it was the first time that allegations of rape were formulated against his client.
Prosecution attorney, Wallace Kapaya, recognized that the indictment did not comprise rape allegations but that the witness had insisted to speak about it.
Since its creation in November 1994, the ICTR has already indicted four catholic priests.
Abbot Athanase Seromba, a vicar in a rural parish in western Rwanda, was sentenced to fifteen years in prison. He has appealed against the sentence.
The trial of Nsengimana resumed on 14 January.
© Hirondelle News Agency