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President Recep Tayyip Erdogan’s decision, published in the Official Gazette on Saturday, says law and communications faculties are to be launched in Bogazici University.
Critics say the establishment of new departments would allow the presidentially appointed rector to staff them with government loyalists. Student groups involved in the protests tweeted against the new decision, saying it was an "occupation" attempt against academic freedoms.
For weeks, students and faculty have led mostly peaceful protests against the new rector, Melih Bulu, who has links to Erdogan’s ruling party.
Read more: Why rumours of a Biden-Erdogan showdown are greatly exaggerated
They are calling for Bulu’s resignation and for the university to be allowed to elect its own president.
Police have detained hundreds of demonstrators at the university and in solidarity protests elsewhere, some taken away following raids of their homes. Most were later released.
Top government officials have said terrorist groups are provoking the protests, and Erdogan has called the protesting students terrorists.
Officials from the United States, the United Nations and the European Union have criticized Turkey’s handling of the protests as well as a series of homophobic comments that were made by Erdogan and other officials while denouncing the demonstrations.