The Queensland skipper carried the problem into the third State of Origin clash and was rested for the Storm's last-round 22-18 win over Gold Coast.
But scans on Monday revealed the extent of a lingering issue, with surgery required on a cartilage injury that could end Munster's season, with the 31-year-old expected to be sidelined for four to six weeks.
Sitting 10th on the ladder, Melbourne are still a chance of playing finals with six rounds and a bye left in their campaign, but the loss of linchpin Munster makes their task much tougher.
They face the third-placed Sydney Roosters on Friday night at Allianz Stadium as well as looming matches against big guns South Sydney, Penrith, Manly and Cronulla.
Tyran Wishart was among the team's best in the tight win over the Titans and centre Nick Meaney said the utility was the perfect player to fill Munster's No.6 jersey.
"It's never nice to see one of your fellow teammates go down and especially this time of year when we need him the most, it's pretty tough," Meaney told AAP.
"Obviously he's (Munster's) a very experienced player, he's played on the biggest stages in the game.
"Bit Wishart's a great player, a great eyes-up footy player just like Mun (Munster), so I've got no doubt that Wishy's going to do a good job while he's in there.
"It's up to everyone else to pick up the load and it's not an individual sport, it's a team sport, so it's not all on one guy's shoulders."
Wishart covered for the injured Munster for eight mid-season matches in 2024, steering the Storm to seven wins as they played their way into a losing grand final against the Panthers.
Meaney said that experience had built belief that Wishart was up to the task, with their 2026 season on the line.
"I think people forget that he had that great year in 2024 when he played most of the year when Mun was out," said Meaney.
"He had probably one of his best years, to date, and that was in the number six jersey, so, I've got full faith with him.
"I've played alongside him before when he's played halfback when (Jahrome) Hughes is out, and he's a great defender and a great runner of the ball."
Meaney himself missed five weeks with a calf injury but returned to play a crucial role against Gold Coast.
He scored in the 79th-minute to break an 18-18 deadlock and secure the Melbourne victory.
"The lungs were hurting and the legs were a bit heavy, but it was good to be back out there," he said.
"I remember thinking in that last four or five minutes, I just didn't want the game to go into overtime because the body wasn't feeling too great, but everyone did their role leading up to it and I pretty much just dove over."
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