The trust which runs the Diana Princess of Wales Hospital in Grimsby and Scunthorpe General Hospital had the worst A&E waiting times in England last month.
NHS England figures show North Lincolnshire and Goole NHS Foundation Trust saw only 53.2% emergency patients within the target of four hours.
The England average for September was 75.2%.
In a statement, Dr Peter Reading, Chief Executive, said: “I want to sincerely apologise to every patient who had a long wait in our departments last month. Our staff in the departments are doing a fantastic job and working extremely hard day in and day out to see as many people as possible as quickly as they can.
"It hasn’t been easy for them – in September our region was seeing higher COVID-19 numbers than almost anywhere else. As well as this the whole of the Humber region’s health system is under pressure – GP services, social care and community care as well as hospitals.
"When this happens A&E departments get very busy and that is what we have been coping with. I would continue to ask our local communities to think carefully about the NHS service which is appropriate for them. If you have an urgent medical problem and you’re not sure what to do, please call NHS 111 for advice from their specialist clinical team.”