"Where is God in the extermination camps? Where is God in the mines and factories where children work as slaves? Where is God in makeshift [migrant] boats that sink in the sea?" Pope Francis said as quoted by NDTV.
The pope also denounced pedophilia and the exploitation of women on Friday, pointing to "unfaithful ministers" who strip the innocent of their dignity.
Good Friday is a Christian holiday that commemorates the crucifixion of Jesus Christ and is part of the Holy Week that culminates in Easter Sunday.
On Holy Thursday, Pope Francis washed and kissed the feet of Muslim, Christian and Hindu refugees in a gesture of brotherhood.
Francis also condemned the Tuesday terrorist attacks in Brussels that took the lives of over 30 people, injuring hundreds of others.