McCann hurt his right ankle in a challenge with Queens Park Rangers striker Andre Gray in the first half of last Saturday's 3-2 defeat at the Kiyan Prince Foundation Stadium.
The 21-year-old tried to play on but was forced to concede defeat a few minutes later and was replaced by Alan Browne.
It was McCann's first Championship start having come off the bench in the previous five league games since a £1.2m move from St Johnstone on transfer deadline day.
He had been due to meet up with the Northern Ireland squad on Sunday ahead of the World Cup qualifiers against Switzerland and Bulgaria during the international break.
They have confirmed that McCann is one of five players to have pulled out of the squad because of injury.
Northern Ireland manager Ian Barraclough said: "We’ve dealt with injuries coming into a number of previous camps and, unfortunately, this one is no different.
"But this is a resolute group that has come together through adversity and I have no doubt they will do it again.
"We are still waiting for a few players to join us and we look forward to a few days training in Belfast before we fly out to Switzerland."
McCann is to have his ankle scanned to assess the extent of the damage.
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