Hebron and Hebron Polytechnic universities in the West Bank remain closed, according to Palestine's deputy minister of higher education, Hisham Kuheil. But nine others were still functioning.
Mr Kuheil said: "Israeli soldiers invaded these two institutions and took computers and documents. There is no proof the institutions were producing terrorist-related material. It's not justified legally."
The two universities have 6,400 of the 80,000 students at universities and colleges in the West Bank. Mr Kuheil said: "The universities are centres for education, not for harbouring terrorists. I am a peaceful man, but you cannot predict people's reactions if they are subject to Israeli humiliation. You cannot close the universities for these actions. Arrest the person, but don't impose collective punishment on institutions."
An Israeli Defence Force spokesman said: "The terrorist organisations have based most of their operational infrastructure on students. The activity of the organisations includes the publication and distribution of incitement materials, recruitment and instruction of hundreds of operatives."
The spokesman said that a Hebron Polytechnic student caused the deaths of seven Israelis at the West Bank settlement of Otniel last December.