The Royal College of Surgeons (RCS) has said the absence of a Stormont executive is "paralysing public services" and "hurting the health of the nation".
It follows the publication of official statistics showing more than 100,000 patients were waiting for treatment for more than a year as of 30 June.
The RCS called for an end to deadlock:
"We fear waiting times in NI will continue to spiral out of control, putting patients at very real risk."
The Department of Health figures, published on Thursday, showed more than 18,000 people were waiting over 12 months for in-patient treatment.
Almost 89,000 were waiting over a year for an outpatient appointment.
By contrast, in England around 3,500 patients were waiting more than a year for treatment.
The RCS said the lengthy waiting lists were a symptom of long-standing problems with the Northern Ireland health service and were not helped by the current political impasse at Stormont.
Responding to the figures, Mr Mark Taylor, RCS Northern Ireland director, said: "Waiting times in Northern Ireland for inpatient and day case treatment are the worst in the UK. Tens of thousands of patients are waiting more than a year for treatment compared to around 3,500 in England.
"The health service in Northern Ireland is facing significant challenges exacerbated by capacity issues, workforce shortages, uncertainty over long-term budgets and the political stalemate at Stormont."
Mr Taylor said the implementation of plans for health service reform were being hampered by the lack of an executive.
"Significant decisions and legalisation are needed to bring about the changes required to address waiting lists and make the NHS sustainable for the future. It is unacceptable for patients to continue to spend many months on waiting lists," he added.
The Health and Social Care Board (HSC) said there was a combination of factors behind the waiting list figures, including an ageing population and an increased demand for services.
It said £30m of additional funding had been made available to address waiting lists in 2018-19.
"Consistent with the approach in previous years, the funding is being targeted at those patients with the highest clinical priority in the first instance and thereafter to assess/treat the longest-waiting routine patients," the HSC said.