Dr Michael McBride said continuing public adherence to restrictions and infection control guidelines was crucial in efforts to prevent a further wave.
Dr McBride said the vaccination rollout would help lessen the dependence on restrictions going forward, but he made clear that Covid-19 would continue to pose a risk in the future.
“I think it is more likely than not that we will see another surge of this virus perhaps towards the autumn time,” he said.
“And I think that we all can take measures to make sure that that isn’t the case.”
The CMO was speaking ahead of a key Stormont Executive meeting on Tuesday when ministers will formally review the current lockdown restrictions in Northern Ireland.
Ministers have made clear that the public should not expect a widespread lifting of measures but they have suggested easements could be announced around certain outdoors activities, including a return to some sports.
Dr McBride, who received his first Covid-19 vaccine on Monday, said it was important that limitations were still imposed on risky activities associated with outdoor sports, such as sharing changing rooms.
He said ministers would seek to make relaxations in areas that “matter most” to society.
“So getting children back to school, engaging in some activity that’s good for all our mental health and wellbeing – outdoor activity, meeting family and friends in a safe way,” he said.
“All of those things are crucially important but they all come with a price, they come with a risk.
“And it’s really important that we continue to follow the advice because you know, this virus is still out there and it is not going away.”
Dr McBride was asked about surging infection rates reported in several European countries such as Italy, France Germany and Poland and whether Northern Ireland could be facing a similar new wave.
“I think that we’re at a very challenging time at present, because obviously people are tired, they’re tired of the restrictions, people are fed up,” he said.
“I’m tired and fed up with the restrictions on my life and I want my old life back as it once was.
“Nonetheless, we are dealing with a much more transmissible variant of this virus and it will spread in situations where the old variant would not have spread.
“Vaccines are a big part of the answer but not the entire answer – not 100% of people will be vaccinated and even everyone who’s vaccinated may not get full protection from this virus.
“And there is absolutely no doubt as we relax the current measures that are in place we will see case numbers increase.
“Hopefully we have vaccinated most of the people who are at greatest risk of going into hospital and dying, people in my age group and younger and older, and therefore we will begin to see less pressures on our health service and hopefully less people getting really sick and less people dying.”
But he added: “We’re far from out the other side of this yet.”