Dr Joe McEvoy says there were already lengthy waiting lists for a number of conditions and treatments prior to the outbreak.
He says a lot of people are putting off getting medical attention at the moment because of the outbreak
“Think what is going to be waiting for us,” Dr McEvoy told BBC Radio Foyle.
“That means people with conditions like diabetes and cancer will be presenting to doctors at a much later stage than they should be,” he says.
“Hospital outpatient clinics and GPs are going to have a big problem with that,” he told the Mark Patterson Show.
“GPs are going to have to try and prioritise but hospitals are going to have a big difficultly catching up.”
Health chiefs have urged the public to continue to go to hospital if they are suffering from a serious medical condition rather than suffer at home fearing they may be putting extra pressure on the health service.
They say all hospitals remain open for anyone who feels seriously ill and they will be treated as normal.#
Meanwhile, Health Minister Robin Swann says an announcement will be made tomorrow about support for the deaf community in the North of Ireland during the Covid-19 crisis.
DUP vice-chair of the health committee Pam Cameron had said there were “grave concerns” that nothing is yet in place, in terms of communication for deaf people who may be affected by the virus.
Mr Swann said there will be a video relay service and an interpreting system, with the details expected to be released tomorrow.
He said his department was working with the Department for Communities and the Health and Social Care Board to get the plans in place.