The 33-year-old has endured a difficult couple of years due to injuries - and hasn't played since Ireland's World Cup win over the USA back in September.
Having initially recovered from a calf problem, Flannery then damaged his back - with the hooker calling time on his career following medical advice.
"I'm very sad to have to announce my immediate retirement from rugby due to injury," Flannery told the club's official site.
"Since my injury at the 2011 World Cup, I've struggled to regain the level of fitness required to play at this level and after consulting with the medical staff at Munster and at Ireland I am announcing my retirement with immediate effect.
"I would like to thank all the medical staff who have worked so hard on my behalf and shown great patience in dealing with me.
"I feel incredibly privileged to have played with so many great players with Munster and with Ireland. To train hard and win trophies for Munster and Ireland alongside some of my best friends has been an amazing experience.
"I'm incredibly grateful for all the opportunities rugby has given me to date and I would like to thank all my friends, family, coaches and team-mates for their support along the way.
"Finally I would like to thank all the Munster and Irish rugby fans who I have been so proud to represent over the course of my career, your level of support has been amazing and I can never thank you all enough. It's been emotional!"
Flannery played 93 times for the province since joining from Connacht in 2003 - however he managed just eight appearances in the past three seasons.
He made a further 41 appearances for Ireland - playing at the 2007 and 2011 World Cups.
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