He had been sprung from the replacements bench coming up to the hour mark, for his first appearance for Munster since their Heineken Cup victory over Toulon at the same venue in October.
Against Toulon he suffered a recurrence of a troublesome injury to his left calf, and this latest injury is a real setback with important games in the Heineken Cup and the RBS 6 Nations Championship looming large on the horizon.
Speaking after the Ulster game, head coach Tony McGahan said: "It's a different calf (injury), not the same one. We'll just have to wait and see.
"Jerry is quite upset and everyone is feeling for him at this point in time. We will get a scan.
"He worked really hard to get back from where he was and there is no doubt he will work really hard to get back from this one as well.
"I haven't gone through the details with him, he just knows it is injured and we will wait and see with the scan."
The scan, which was taken yesterday, has shown a tear in Flannery's right calf muscle which will rule him out of action for four to six weeks.
That means he will miss Munster's final pool games against Toulon and London Irish and Ireland's RBS 6 Nations openers against Italy and France.