The west African nation has a history of religious tolerance, but there has been a spate of anti-Christian attacks this year.
“May the merciful God gather to himself all who have died while at their Friday prayers and console those who have been hurt. I ask that they be remembered in our churches this weekend.”
The victims were Ethiopians migrants attempting to escape poverty in their home country by making their way via Libya to Europe.
Don Benoît Kinalegu first reported the Lord's Resistance Army massacre of 2008 in which more than 800 people were killed in the region of Haut-Uélé.
Amnesty International warns that Boko Haram has deliberately targeted civilians through raids and bomb attacks, both of which have been increasing in frequency and severity.