Students had been told to vacate the Eastern Cape university because of labour trouble, said administrator Lourens van Staden.
The Pan Africanist Congress (PAC) in the Eastern Cape said it was absurd that higher education minister Blade Nzimande had not intervened in the five-week long labour impasse.
"This means the university has not engaged into its core business of teaching and learning for more than a month now," the PAC said in a statement.
Including the time lost during student strikes at the beginning of the year and more recently, the university had lost more than two months of teaching time.
The Congress of the People Student Movement (CSM) called for an immediate intervention at the university, which serves some of the country's poorest communities.
"We are not treated in the same way as the other 22 universities in South Africa, and sending students home is not a solution on the matter," CSM student movement said in a statement. "Rather address what is needed to be done."
The South African Students' Congress (Sasco) said it was disgusted at the decision to close the university.
"We call on the administrator to reverse this ridiculous and misguided decision," it said.
"Students of Walter Sisulu University have never been harmful to themselves and to the various communities they are staying in. [They] have been engaged in various peaceful protests insisting that they want to go back to class."
Sasco said the labour impasse and the students' past complaints had been proof of the university administration's failures.
The Pan Africanist Student Movement of Azania said the university's closure was a direct consequence of a lack of leadership by Van Staden and the department of higher education. – Sapa