The South African bishops' conference released a statement following the shooting of Fr. Pugin, extending their "sincere sympathy and prayers for a speedy recovery" for the priest who was "offering refuge to frightened students."
The bishops added that while they support the students' right to demand a good and affordable education, they do not condone the violence and looting associated with the protests.
They also said they believe the best course forward is for students and educators to continue with the academic year while working out a compromise for the future.
"...the solution suggested by the students at the moment is beyond the financial and organizational capabilities of university authorities. However, it must remain on our agenda as the priority for the future," the bishops wrote.
"What is to be done is for the government to ensure that this academic year is completed in peace. The government and students must now iron out their difficulties. A compromise must be considered as the huge financial demands of university free education cannot be found instantaneously."
South Africa's government had proposed a similar tuition hike of 10-12 percent in 2015, but froze fees after similar protests.
The student protests are the country's largest since the 1994 end of apartheid. According to the BBC, protestors claim the rate hikes are discriminatory against black students, as the average income of black families is much less than that of white families in South Africa.
In a Sept. 27 statement, the South African bishops' conference had voiced hope that there would be found "a realistic plan of making it possible for the poor and working class families to have access to higher education after the year 2017" and that the private sector would "look into other ways of increasing their financial support to make education affordable to the poor and working class families."