The General Medical Council (GMC) has placed the £842 million hospital under 'enhanced monitoring because there are not enough doctors available to care for patients - making it an 'unsafe' working environment.
This means the internal medicine department which has 93 junior doctors will be subject to a stringent programme of inspections in an effort to improve standards.
The GMC only steps in to provide enhanced monitoring in exceptional circumstances where there are concerns about patients and doctors.
It could impose conditions on doctors' working conditions or even withdraw its approval of the medicine department as a training site which would mean it loses junior staff - if standards are not improved.
The GMC said it 'won't hesitate to take whatever action may be necessary'.
It is the latest crisis to hit the flagship hospital which opened in 2015.
Scottish Tory health spokesperson, Miles Briggs, said: "This is a deeply alarming development in what has been a catalogue of problems.
"I will be raising this with the SNP Health Secretary Jeane Freeman and the local health board at the earliest opportunity."
The internal medicine department includes the Acute Receiving Unit (ARU) and the Immediate Assessment Unit (IAU).
A damning inspection report by the Scotland Deanery of NHS Education Scotland (NES), which oversees medical education, and the GMC reveals a catalogue of concerns.
These include patients whose care was 'significantly delayed'.
Junior doctors said the IAU, which takes patients sent by GPs, is 'overfull' all day and there was a 'lack of support' out of hours by senior staff.
The Scotland Deanery Quality Management Visit Report states, despite some improvements, there are 16 requirements where 'GMC standards were not being met'.
These include a 'general lack of a culture supporting education and training ' which must be addressed as a matter of urgency as well as 'levels of staffing'.
The report adds: 'Trainers (consultants) raised concerns about patient safety within the IAU out of hours'.
The GMC has the legal power to impose conditions on the approval of junior doctors at the hospital if health chiefs do not address the concerns.
QEUH is the subject of an independent inquiry after the deaths of three patients linked to hospital-acquired infections.
Lewis Morrision chairman of the British Medical Association in Scotland said the 'knock-on effect of the staff shortages this report details on the safety of care is a concern'.