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.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.