The Magners League pace setters stretched their lead at the top of the table thanks to three late tries but their 10th win of the season was marred by Flanerry's unfortunate departure in Limerick.
Flannery came on as a second-half replacement for Damien Varley in the Round 12 encounter but he was helped off with just moments remaining of the four-try triumph.
The 32-year-old appeared to injury his calf, although not the same one that has sidelined him for much of the season so far.
Both Munster and Ireland are now awaiting the results of a scan, with Munster head coach Tony McGahan offering Flannery his full support but unable to give any more information on the extent of the injury.
"He's quite upset and everybody is feeling for him," said McGahan.
"He's worked really hard to get back to where he was, and there's no doubt that he'll get back from this one as well."
Flannery was making his first Magners League appearance of this term and had already seen his first comeback blighted by a reoccurrence of his initial injury in a European tie against Toulon in October.
Having been selected for the 2009 Lions tour of South Africa, Flannery missed out on representing Britain and Ireland's elite after injuring his elbow during pre-tour training at Pennyhill Park and has been a peripheral figure for province and country ever since.
He featured just three times in the Magners League last season due to elbow and calf issues, as well as a suspension picked up from the Six Nations defeat to France, and could now be faced to spend even more time on the sidelines as Ireland look for a repeat of their Grand Slam heroics from two years ago.