The singer has been playing through the pain on the band's current North American tour with Dethklok, All That Remains and Black Dahlia Murder after suffering a double inguinal hernia.
Flynn had been planning to wait until January (13) to have surgery to treat the condition, but he now has to undergo an emergency operation after suffering complications.
He will have the surgery on Wednesday (14Nov12) in Minneapolis, Minnesota before heading home to California to rest.
The band has axed nine dates and hopes to be back on the road with Flynn for a show in Portland, Oregon on 24 November (12).
Flynn says in a statement, "I've been toughing out an inguinal hernia below my waistline since June of last year... It hasn't been that painful, and I've gone to the doctor a few times to take care of it, but he said after surgery I probably couldn't sing for a few weeks, and since that wasn't going to happen, I scheduled it for January when I had a break.
"Unfortunately, after the last few shows, my guts have been very swollen and hard to push back in. Yesterday, the pain was excruciating and I went to the emergency room last night. They said that I need surgery.
"I will be doing my damnedest to rejoin the tour in a couple (of) weeks. Thanks to all the fans, bands, and crew for understanding. I'm determined to see you all soon and finish what has been a great freakin tour!"