The defendant allegedly watched as the victims were crushed by the collapsing church, and then oversaw the hunting down of others by armed gangs.
The incident is believed to have happened during the 1994 Rwandan genocide, which lasted 100 days and saw the massacre of more than half a million members of the Tutsi ethnic minority.
Even though the case is 15 years old, the chaos and widespread brutality of the genocide means that justice is still being sought today.
The defendant, Gaspard Kanyarukiga, was arrested in South Africa in July 2004. He has pleaded not guilty to the charges against him.
The prosecution alleges that Kanyarukiga forced a reluctant bulldozer driver to smash down the church where 2,000 Tutsis were seeking refuge.
Hundreds were killed in the demolition and those that escaped were quickly slaughtered mercilessly.
The Tanzania-based International Criminal Tribunal for Rwanda is conducting the trial. It has tried 39 people since it was set up in 1994.
It is thought that Kanyarukiga’s trial could take years to come to a conclusion.