Two universities - the University of Greenwich and Leeds Metropolitan University - have received "limited confidence" ratings from the Quality Assurance Agency.
The standards watchdog says it has only limited confidence in "the soundness of present and likely future management of academic standards" at each institution.
The ratings, published in audit reports, follow criticism of the QAA, which has been accused of failing to adequately safeguard standards.
In a report this summer, MPs on the Innovation, Universities, Science and Skills Committee say the QAA "focuses almost exclusively on processes" and that, in not judging standards directly, it takes "an unduly limited view of its potential role".
In an audit report published on 9 October, the QAA criticises Leeds Met for inconsistencies and contradictions in its academic regulations. It says they are "not fit for purpose or accessible for staff".
The report also notes "with concern, evidence of inconsistent application of process between faculties, particularly in programme approval, monitoring and review".
Courses have been running for more than five years without review, and the involvement of external academics in the review process is "not always critical and robust", it says.
It adds that a policy of not involving external reviewers when courses are changed unless at least 30 per cent of modules are affected is "putting standards at risk".
Geoff Hitchins, acting vice-chancellor of Leeds Met, said he was not surprised by the findings. "When I came into the university, it was not at ease with itself," he said.
Dr Hitchins was appointed in January after the resignation of Simon Lee.
He said he had immediately instigated a review of the student experience and academic quality and "moved the emphasis away from events, partnerships and festivals towards core objectives".
"I told the QAA at the time of the audit in May that I wasn't entirely satisfied with the consistency of our approach," he added. "I'm confident that when the QAA returns, it will find that all the issues have been addressed."
The standards watchdog also criticises Greenwich. In a separate audit report, it says the introduction of new student assessment measures has led to an increase in first- and upper-second-class awards.
It identifies inconsistencies in the way the new methods have been applied, which it says has resulted in 7 per cent of students receiving higher marks than they deserved.
The university is also criticised for claiming that all its awards are covered by the Framework for Higher Education Qualifications.
In fact, two awards given to students who fail to complete courses - the Greenwich "diploma" and "certificate" - do not comply with the framework, the QAA says.
A spokeswoman for Greenwich said action was being taken "to fully address the points raised" and pledged to "go further to ensure that our quality assurance processes build on the guidance given and further enhance our students' teaching and learning".