Education Cabinet Secretary, George Magoha, has placed JKUAT PhD holders under probe over a recent damaging report, released on Tuesday.
All students who were awarded a doctorate since 2014 could risk a recall of their accreditation.
The Commission for University Education (CUE), directed the Juja based campus to reassess all the degrees conferred for possible breaches.
JKUAT now has three months to compile their comprehensive report and table it before the commission.
Some of the breaches mooted by the commission include the supervision of 13-14 students by a single lecturer, contrary to the recommended maximum of 3 students per lecturer.
"I suspect it is not just at JKUAT," CS Magoha remarked during his address to the press.
The CS through the CUE also banned the university from admitting doctorate students in any of its satellite campuses.
This was after the damning report revealed that more than half of all the doctorate students had graduated from these satellite campuses, over insufficient capacity.
"The university should cease training PhD students on the satellite campuses for lack of adequate capacity and transfer them to the main campus in Juja," an excerpt of the report revealed.
Reports by the Standard claimed that the probe was instigated by the high number of PhDs awarded this year, particularly in the College of Human Resource Development.