Racist harassment of Papuan students in university dormitories in Javanese cities last month sparked weeks of widespread protests and unrest in Papua.
While Indonesian police have started investigations into the harassment, many students claim they continue to face threats and feel unsafe.
As of Monday, 2047 students had been recorded by Papua's provincial government as having left their studies to return to their home region since August.
The majority of the students are from Highlands regencies in Papua.
Last month, in response to the harassment, Papua's Governor Lukas Enembe offered support to students who wished to return home from Java.