He, however, did not specify whether irregularities or shortcomings were found in the others.
Raju said 98 private universities have been established in the last four years.
Explaining the procedure, he said UGC gives time to universities to rectify any deficiency. If norms or guidelines are not followed, "UGC can order closure of courses but it has no power to close the universities."
Private universities can be established either by the central government by an Act of Parliament or by state governments by an Act of state legislature.
"All private universities existing in the country have been set up by the Acts of State Legislature and the norms and parameters to establish private universities are decided by state governments concerned," he said.
Though UGC sets norms for standards of teaching and examinations, neither "UGC nor the HRD Ministry has any power to approve or disapprove a private university duly set up by a state through a state Act," he said.
The government, he said, can deal with malpractices and take action against universities and institutions after passage of the Prohibition of Unfair Practices Bill and the Regulatory Authority Bill.
"These Bills will strengthen cause of quality education," he said, adding UGC will expedite investigation of malpractices.