The University of Delhi (DU) requested intervention from the University Grants Commission (UGC) in the appointment of Professor John Varghese as the principal of St Stephen's College, claiming that his appointment is "ultra vires" of the provisions of the commission's act. Varghese's five-year term as college principal ended in February of last year and the university is "constrained" from recognising him as such, according to a letter from the university's Assistant Registrar to the Secretary of the UGC. The letter stated that, "The intervention of the UGC is very kindly solicited to preclude any act of defilement of UGC regulations by St  Stephen's College and other colleges as well,'' stated a report by The New Indian Express. 

Varghese was appointed as St Stephen College's Principal in March 2016 for a five-year term, after which the college's Supreme Council extended his appointment. Prior to the admissions process by DU, the university and Varghese had been at odds for a number of months over the admissions policy following the introduction of the CUET. According to the university, it has claimed that the college has been repeatedly justifying the reappointment of Varghese by citing the resolutions of its Supreme Council, stated The New Indian Express report.

However, under the regulations of the UGC, there is no provision for a council. The university also stated that, "It may be noted that the UGC Regulations, 2018 does not provide any exception to any category of educational institutions from complying with the norm for reappointment of principal or have a different provision for reappointment of principal, after completing the first term through anybody. Accordingly, such act of reappointment/extension of the term of Varghese by the so-called Supreme Council of the college is ultra vires of the provisions of the act, statutes and ordinances of the University/UGC regulations referred above," added the university in the letter. 

The University declared Varghese's reappointment as the college's principal to be "null and void" in a letter to St Stephen's Governing Body Chairman Prem Chand Singh in August, claiming that it was not done under the law.