Mr Javadekar said the government has no intention to change the names of AMU and BHU.
The panel, which was formed to probe the alleged irregularities in 10 central universities, has made the recommendation in its audit report on the AMU.
"AMU and BHU are very old institutions, and we do not intend to change their names. We formed a committee to look into the administrative, academic and research audits of universities.
"The mandate of the committee is to look into the administrative, academic and research audits of universities. We will not take cognisance of what they have recommended outside of this," Mr Javadekar told reporters in Ahmedabad.
While maintaining that he has not seen the panel's report, he clarified that "there is neither such decision nor is there any such intention to change the names".
According to the UGC panel, the universities can be simply called Aligarh University and Banaras University or be renamed after their founders.
Centrally-funded universities are secular institutions but such words related to religion in their names do not reflect that character, a panel member said on the condition of anonymity.
Besides AMU and BHU, other universities that were audited by the panel included Allahabad University, Hemwati Nandan Bahuguna Garhwal University in Uttarakhand, Central University of Jharkhand, Central University of Rajasthan, Central University of Jammu, Mahatma Gandhi Antarrashtriya Hindi Vishwavidyalaya in Wardha, University of Tripura and Hari Singh Gour University in Madhya Pradesh.