The standards watchdog was called in to investigate the University of Bedfordshire after an external examiner complained about the case of a doctoral student whose appeal against a "fail" judgement was upheld by the university.
The examiner said Bedfordshire had contravened its own code of practice by failing to discuss with the original panel of examiners how the appeal might be resolved.
External examining was also undermined because the institution failed to explain to the examiner why the candidate's work - a PhD by publication - had been referred to appeal, it was claimed.
After its investigation, the QAA highlighted several flaws in Bedfordshire's procedures.
Its report finds that the appeal hearing was not conducted impartially, with the panel's chair able to "disproportionately influence the process and outcome" because the same person also chaired the postgraduate awards committee.
Deliberations on the evidence by the panel were, according to the formal record, superficial and uncritical, it adds.
Bedfordshire's requirements for a PhD by published work were also unclear to all concerned, the regulator says.
The QAA has made four recommendations and ordered the university to draw up an action plan to address its concerns.
A university spokeswoman said the regulator had not questioned Bedfordshire's academic standards but rather criticised its procedures.
"At the time, we did not have a process in place for handling PhD appeals specifically, mainly because they are extremely rare: in fact, we had never had any such appeals," the spokeswoman added.
"So, in the event, we followed our normal appeals procedure and gathered together a new panel of examiners to reassess the work.
"We are grateful to the QAA for pointing out this omission and have now put in place a comprehensive PhD appeals procedure."