The violence towards the Catholic Church in the country was sparked following the Church providing humanitarian assistance in its parishes in a bid to diffuse a worsening political crisis.
Sunday was the deadliest day in the Central American country since the protests began with 38 people being killed during clashes in three areas, according to the Nicaraguan Centre for Human Rights (Cenidh).
Bishop Silvio Jose Baez and at least one other priest were injured as they attempted to protect St Sebastian Basilica in the city of Diriamba from a pro-government mob.
Journalists were also attacked and had cameras and other equipment stolen, the Tablet has reported.
Asediado por una turba enardecida que querÃa ingresar a la BasÃlica San Sebastián en Diriamba, fui herido, golpeado en el estómago, me arrebataron las insignias episcopales y agredido verbalmente. Estoy bien gracias a Dios. Se liberó la basÃlica y a quienes allà estaban. pic.twitter.com/9qTgugBjic
— Silvio José Báez (@silviojbaez) July 9, 2018
"I was injured, punched in the stomach, they took my episcopal symbols away from me, and verbally attacked me," Bishop Baez tweeted, with a picture of a wound on his arm and blood-stained habit.
"I'm OK, thank God. The basilica is free and so are those who were inside."
The bishops and clergy tried to free anti-government protesters inside the church which was reported by pro- government media as proof that the Church allows weapons to be stored inside its properties.
The Catholic Church, which has been acting as a mediator in stalled talks between the government and the protesters, has denounced the violence.
More than 300 people are reported to have been killed since the the protests against the government was triggered by changes to the social security system announced on 18th April.
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