The 32-year-old Belgian has struggled to train properly as the cyst is located where he sits on the saddle.
"Though the perineum cyst that has been tormenting him for the past few weeks is shrinking, it is still very painful and the wound ... has not completely healed," his team said on their website.
Boonen added: "It's terrible news but unfortunately I was expecting it ... The team staff and I have agreed to give the injury time to heal and then in October I will immediately start preparing for 2014."
Boonen, who won the world road race title in 2005 and the Tour de France points classification two years later, is one of the most successful riders despite having been in trouble after failing a dope test for cocaine in 2008.
He shares records of wins on some of the best-known cycling classics including Paris-Roubaix, where he has triumphed four times, and the Tour des Flandres.
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