A Medical Council inspection of nine hospitals has found that some interns were asked to perform duties above their grade.
It says some trainees at Galway University Hospital alleged they were also left unsupervised when a consultant was absent for a week.
However, the report says that the hospital was complying with required criteria and the trainees knew who their clinical supervisors were.
At other hospitals, the council found that medical registrars refused to write notes in patients' charts and left this to interns to complete, regardless of whether they had seen the patient or not.
Some trainees were taking consent from patients, when unqualified or untrained.
Allegations of bullying were also made by some interns and non-consultant hospital doctors (NCHDs).
At Letterkenny University Hospital, inspectors found signs on a radiology department door saying 'no NCHDs' and asked that they be removed immediately.
In one site, male interns reported receiving preferential treatment from nurses, compared to that of their female colleagues.
Poor Wi-Fi or no Wi-Fi and a need to upgrade on-call accommodation facilities at a number of sites were also issues.
The council has published the first reports into inspections carried out in 2017 in hospitals across the Saolta University Health Care Group and the South/South West Hospital Group.
The inspections examined training for interns and specialist trainees.
The Saolta Group was 64% compliant with training standards for interns and over 30% compliant for specialist training.
The South/South West Hospital Group was 34% compliant for interns and 23% compliant for specialist training.
The council has expressed concern about service delivery being prioritised over education, due to a lack of resources, which it said apparently cannot be controlled by individual clinical sites or hospital group management.
Una O'Rourke, Director of Education, Training and Professionalism at the council, said that although the nine hospitals were, for the most part, found to be at least partially complying with standards, numerous similar issues arose across many of the clinical training sites.
The council said that all of the hospitals inspected should continue to provide medical education and training to interns and specialist training to NCHDs.
The hospitals in the Saolta Group were: Galway University Hospital, Letterkenny University Hospital, Portiuncula University Hospital and Sligo University Hospital.
The hospitals in the South/South West Group were: University Hospital Kerry, South Tipperary General Hospital, Mercy University Hospital, University Hospital Waterford and Cork University Hospital.