Flannery, who turned 32 on Sunday, has been dogged by hamstring and calf injuies in recent months. He made his comeback for Shannon last week in the All-Ireland League, lining out for 40 minutes in their Division 1A win over Garryowen.
He was back at Thomond Park on Saturday to earn his first provincial cap since last May's Heineken Cup semi-final defeat to Biarritz Olympique.
However, it now looks like he may face more time on the sidelines and his participation for Ireland in next month's GUINNESS Series is in serious doubt.
Speaking after Saturday's game against Toulon, Munster coach Tony McGahan said: "It's certainly unfortunate if it is (a recurrence of the injury) because Jerry has worked so hard to get back.
"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."
Meanwhile, full-back Paul Warwick, who limped off in the 64th minute of the Toulon match, is not thought to have suffered a serious injury. He is expected to be available for next weekend's Magners League game against Benetton Treviso.