It is rotten luck for the 32-year-old who had was just coming back to full fitness following a calf injury.
The Ulster match was only his second appearance in a Munster shirt this season, having also come on in the Heineken Cup clash with Toulon, but was hoping to be eased back into action before the Championship.
But the scan revealed Flannery will be out for up to six weeks which would rule him out of the matches against Italy and France as well as Munster's remaining Heineken Cup matches.
That leaves the Irish province with just two registered hookers for the rest of the tournament and Munster boss Tony McGahan admitted after the match his absence will be a huge blow.
He said: "It's a different calf (injury), not the same one. We'll just have to wait and see.
"He 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."
Rory Best, most likely to fill Flannery's shirt, is on the comeback trail since fracturing a cheekbone during the November Test series.