Munster was a stand-out for the Storm last week in the No.1 jersey, scoring a hat-trick in his first NRL game at fullback since the start of 2018.
But Hughes' shoulder injury has prompted a return to the halves for Thursday night's blockbuster match against ladder leaders Penrith, with Nick Meaney back from concussion to resume the fullback role.
The Storm have also welcomed centre Justin Olam back from COVID isolation, but are without second-rower Felise Kaufusi following the death of his father.
Penrith are also some chance of getting Viliame Kikau back from a hip injury, with the Fijian international named on an extended bench.
Fellow top-four team North Queensland have been handed a pre-finals boost, with prop Jordan McLean back from a hamstring injury.
McLean has not played since being called into the NSW team for the State of Origin decider, only to be injured in training in the build up.
Kyle Feldt is still sidelined for the Cowboys' bumper clash with the Sydney Roosters, with Hamiso Tabuai-Fidow to stay on the wing.
Canberra have copped a blow with form forward Joseph Tapine to miss Sunday's must-win clash with St George Illawarra with a rib injury.
Newcastle have welcomed forward David Klemmer straight back into their team to play Brisbane, while Adam Clune replaces Jake Clifford in the halves.
Cronulla remain without Matt Moylan for their trip to Tamworth to face Wests Tigers, with the Sharks taking a cautious approach on his quad injury.