The CMJ University was officially established as a recognized, private university in Meghalaya State in July 2009.
In April / May 2013 CMJ was investigated when officials in neighboring Assam State filed a complaint. CMJ University was accused of being in violation of UGC rules by setting up distance education centers, and not meeting the minimum standards for award of MPhil/PhD degrees. The university registrar and deputy registrar were arrested, and the chancellor went into hiding from law enforcement.
CMJ University awarded 434 PhD degrees in 2012 with only 10 professors with PhD degrees on staff. The Governor of Meghalaya State ordered that further admissions should be suspended, tuition payments refunded, and all degrees awarded previously be withdrawn. The university was also directed to provide the names and addresses of all PhD degree recipients.
In September 2013 Indian Supreme Court dismissed petition filed by CMJ University Chancellor, and directed Meghalaya State to carry out the Governor's order to dissolve the university within three months.
In October 2013 CMJ University Chancellor was investigated by the Indian CID (Crime Investigation Department). After this preliminary questioning, the Chancellor again fleed law enforcement. The State of Meghalaya requested that the Supreme Court resccind the chancellor's interim bail.
At Present Time CMJ University remains on the UGC list of private universities, with a caveat regarding proposed dissolution.