President Maithripala Sirisena said steps would be taken to bring the organization referred to as the Sharia University in Batticaloa under the control of the Higher Education Ministry.
Sirisena also said that its academic activities and syllabus would be streamlined and regulated.
The University Grants Commission (UGC) in a statement said that no organization has been given the authority to conduct degree courses at a university known as the 'Sharia University' or the Batticaloa Campus.
"As per the University Act of 1978 (as amended), the University Grants Commission is mandated only to plan and coordinate University education and regulate administration of 15 state universities that come under the purview of the University Grants commission," the statement said.
It was widely speculated that the so-called Sharia university would be used to propagate extremist religious views in Sri Lanka.