Prof Ian Young said about 18 per cent of adults have still not come forward for their first dose of a Covid-19 vaccine.
It comes as Health Minister Robin Swann said first doses of the vaccine will end at the North of Ireland’s mass vaccination centres on Saturday, July 31.
Mr Swann said the vaccination programme would not be available indefinitely.
As of Monday afternoon, 2,168,431 Covid-19 vaccines had been administered in Northern Ireland.
Of those, 1,185,869 were first doses and 982,562 were second doses.
The North of Ireland’s rate is the lowest in the UK.
Referring to those who had not come forward for vaccines, Prof Young said: “That means 18 per cent who are just as susceptible to the most severe effects of Covid as they were earlier in the epidemic.”
He said he was also very concerned about the rise in cases and hospital admissions in the North of Ireland.
“Pressures on our hospitals have been very significant all through the summer for multiple reasons,” he said.
“Certainly adding a significantly increased number of Covid admissions on top of that is going to bring considerable pressures to bear and I know our hospitals are thinking carefully about how they can best manage and cope with that as we go through the next six to eight weeks.
“Unfortunately I think that there will be some increases in deaths, which is inevitable as a result of a very large number of cases leading to quite a large number of hospitalisations and patients in critical care.
“But the number of deaths, the proportion of deaths from Covid, will be much less than in previous waves of the epidemic as a result of the impacts of vaccination and of improved treatments, which have gradually come into place during the last 18 months.”
On Monday another 1,776 positive cases were reported by the department on Monday. This included samples taken in recent days, not necessarily in the previous 24 hours.
There were 109 inpatients with a confirmed diagnosis of Covid-19 in Northern Ireland’s hospitals, with seven patients in intensive care units, three of whom were on ventilators.
The Department of Health is continuing to operate a number of walk-in Covid-19 vaccine clinics across Northern Ireland this week.
The appointment-free pop-ups were established as part of a “final push” to get younger people vaccinated.
Chief medical officer Sir Michael McBride said young people presenting for first doses in Northern Ireland is lower than other areas of the United Kingdom.
Sir Michael said today: “Unfortunately, over the past number of weeks, the number of people presenting to get a first dose of the vaccine has slowed quite significantly, particularly in the younger age groups.”He added: “There is 6% more people in England, eight percent in Scotland and 10% more in Wales.”
Sir Michael also discouraged young people from believing false vaccine rumours circulating on social media.
He estimated, based on current modelling, that by the end of this month Northern Ireland may exceed “over 2,000 Covid-19 cases a day” and “by the middle of August that could be anywhere between 3,000 – 4,000 cases”.
He said if the North of Ireland could increase the number of people getting their first doses by 5% it could could reduce the number of new cases by half.
The chief medical officer said that the Joint Committee on Vaccination and Immunisation (JCVI) has provided interim advice on a booster vaccination programme in the North of Ireland.
He said it could be rolled out for over-50s and clinically vulnerable people from September.
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