The Meghalaya governor's secretariat had lodged a first information report (FIR) with police against the CMJ University and its chancellor Chandra Mohan Jha for alleged lapses and fraud.
"We have seized over 7,000 PhD thesis from two different CMJ university campuses located in Shillong and Jorabat," a CID official told IANS.
The seizures were made a week after the Supreme Court had granted partial relief to Jha, who is still at large. The court said he will be given bail in the event of his arrest.
The university was established by an act passed by the state legislature in 2009 while it started functioning from Oct 17, 2010. It is alleged to have issued a large number of fake PhDs.
Each student desiring to pursue a Ph.D. programme from the university would have to pay Rs. 1.27 lakh.
"We suspect that the Ph.D. theses were printed in Calcutta as the print and design were identical," the CID official.
The CMJ varsity has created a record of sorts by awarding PhD degrees to 434 candidates in the 2012-13 academic year. It enrolled 490 students for the PhD programme during 2012-2013.
What was significant is that only 10 of its faculty members have doctorate degrees.
Former governor R.S. Mooshahary, in his capacity as visitor of the varsity, had exposed irregularities in its functioning and asked the state government to dissolve it
Deputy Chief Minister R.C. Laloo, who holds charge of education, said that the state education department had slapped a show cause notice to the university asking it why it should not be dissolved.
The University Grants Commission (UGC) had also constituted a nine-member expert committee headed by Tezpur University Vice Chancellor Mihir K. Chaudhury to look into alleged irregularities committed by the private university.
CMJ University had been running distance education centres outside the state, in other parts of the country, as well as in some centres abroad, in breach of University Grants Commission regulations and guidelines.