Nearly half of trainee doctors working in NSW hospitals say they have made a medical mistake because they were tired from working long hours, as the COVID-19 pandemic continues to strain the health system.

Nearly 1800 NSW doctors-in-training responded to the Australian Medical Association annual survey, with 46 per cent of them admitting they had made a fatigue-induced error - an eight point increase on last year's Hospital Health Check.

The number of doctors who were concerned for their own safety due to fatigue associated with long hours increased to 56 per cent from 47 per cent last year.

AMA NSW doctors-in-training committee co-chair Sanjay Hettige said the Omicron wave had "wiped out the workforce" in NSW hospitals.

Staff furloughs meant longer hours for trainee doctors who were forced to cover shifts for sick colleagues.

"When there is this much pressure on the health system both the safety of patients and doctors is compromised," Dr Hettige said in a statement on Monday.

"The risk of human error increases with fatigue. Small mistakes such a medication errors or poor communication during handovers can have ramifications.

"There is also the risk of staff becoming burnt out or suffering from poorer mental health, which we know can lead to higher rates of doctor suicide."

The survey also recorded a significant jump in the number of respondents working more than five hours of unrostered overtime - 72 per cent, up from 60 per cent last year.

A further 53 per cent rated their inpatient workload as heavy or very heavy.

There was tremendous pressure across the system and doctors-in-training were "at the coalface" as more people presented at public hospitals, patients were sicker and stayed longer, Dr Hettige said.

"We are working harder and longer.

"NSW risks losing doctors-in-training to other states that offer better entitlements."