It is the latest in a long list of injuries to have hit the hooker and Flynn admitted this latest setback, which sees him miss the Crusaders trip to South Africa for matches against the Bulls and the Stormers, was "annoying".
In 2003 his Super 12 season was disrupted by a broken arm.
And last year he dislocated a shoulder but recovered in time for New Zealand's tour to Europe only to damage his hamstring.
"I was just hoping to get through the season without an injury," he told One Sport.
"That was actually the biggest thing for me, so it's frustrating to have this happen now after I'd got through six rounds."
Flynn suffered the injury in a maul following a line-out.
"I knew straight away I had done something. I thought I might have snapped a rib. I remember Dave Hewett was yelling at me to get up and I couldn't. The play went left and I stood up and I couldn't breathe and I couldn't yell at Steve Muir, our physio.
"It was like that feeling when the breath is sucked out of you when you hit really cold water and you can't do anything. I knew then I'd done something bad to my ribs.
"Every time I take a deep breath or sneeze or cough, it hurts so it's not great."