Flannery appealed the six-week suspension imposed on him by a Six Nations disciplinary committee which upheld the citing against him for kicking an opponent in Ireland's Six Nations clash with France at the Stade de France last month.
In handing down the six-week suspension originally, the disciplinary committee took account of the guilty plea by the player, who acknowledged at the outset that his action warranted a red card, together with the player's remorse for the injury caused to Alexis Palisson, the France winger. Palisson was subsequently forced to leave the pitch with a dead leg.
However, an independent Six Nations appeal committee, chaired by HH Judge Jeff Blackett (England) and also comprising of Douglas Hunter (Scotland) and Marco Cordelli (Italy) dismissed Flannery's appeal when it was heard at a Heathrow hotel on Wednesday.
The appeal committee also dismissed the cross-appeal made by the Six Nations Disciplinary Officer, which, if successful, could have resulted in the length of the hooker's ban being increased.
The appeal committee upheld the original disciplinary committee's finding that the act of foul play was in the mid-range of offending defined by IRB Regulation 17 and that the level of net mitigation applied was within the correct margin of appreciation.
As a result, Flannery will miss Ireland's RBS Six Nations Championship fixtures against Wales at Croke Park on March 13 and against Scotland at GAA headquarters a week later.
Munster and Ireland star Flannery is free to commence playing again on Monday, March 29, ahead of Munster's Magners League clash with Leinster at Thomond Park on Good Friday.