The 22-year-old suffered the injury during Saturday's win over Wycombe Wanderers but the true severity did not come to light until afterwards.
McCann says Rovers will not know the timeframe on his return until after the results of the scan but said Kiwomya will not play in Tuesday night's Carabao Cup clash with Scunthorpe United.
"We'll be without Alex Kiwomya, who has felt his hamstring, which we don't know the extent of just yet," McCann said.
"He'll go for a scan today [Tuesday].
"It's disappointing to lose Alex. It was his first start.
"By all accounts he did in early in the second half, didn't really say anything and carried on.
"We'll see how he is over the next couple of days but apart from him everyone is good."
McCann insists he will not be resting players in cup competitions but confessed one player who did start Saturday's game will sit out the Scunthorpe trip entirely as the Rovers boss looks to manage his game time.
Niall Mason is available for selection despite being withdrawn with cramp during the win over Wycombe.