Published Thursday, 22 October 2009
But worst case scenarios have been revised downwards, Dr Michael McBride added.
Young people are particularly at risk because they have not been able to build up immunity from previous pandemics, he said.
There were three swine flu-related deaths in Northern Ireland announced on Wednesday night including a second pupil at a Londonderry special needs school.
Dr McBride said: "It is going to be a long, a difficult winter. It could be one of the most difficult winters we have seen."
The senior medic gave evidence to Stormont's health committee.
'Unpredictable'
He warned Northern Ireland avoided the worst of the first wave of infections last spring but that may mean more people were vulnerable this time round.
"We could see this virus being around for very many months and into next year as well," he added. "They are totally unpredictable, they mutate, they change."
Figures out on Thursday show the estimated number of new cases of swine flu almost doubled this week, raising fears that increasing hospital admissions will put pressure on NHS beds.
The number of deaths across the UK has risen to 122 - 93 in England, 15 in Scotland, eight in Northern Ireland and six in Wales.
England's Chief Medical Officer Sir Liam Donaldson said he was concerned by the high proportion of deaths in younger age groups, describing it as a "very unusual pattern for flu".
More than half (54%) of deaths have been in the under-45 age group while 77% have been in the under-65 group.
With seasonal flu the majority of deaths would be expected in the over-65s.
One in three deaths related to people who had little or no underlying health problems.