Flannery, who turned 32 yesterday was taken off shortly before the full-time whistle with a suspected calf injury and now must agonisingly wait to see a specialist later this week.
"It's certainly unfortunate if it is (a recurrence of the injury) because he has worked so hard to get back," Tony McGahan.
"He missed a significant part of last season and this was his first foray back into selection. So to be injured in the first 15 minutes of his comeback is devastating for him."
Only last week Flannery spoke of his 'delight' to be returning but this latest injury could now rule him out of Ireland's autumn international campaign.
"Everything has gone well so far," said Flannery before the weekend's fixture.
"There is a lot of rugby to play. The trick now is to try and stay fit. There is a lot of competition everywhere for places. If you are not fit, you are not even considered."