Munster was a standout 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 at fullback.
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 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.
Egan Butcher returns for the Roosters in what will be captain James Tedesco's 200th NRL match.
Canberra have copped a blow with a rib injury ruling out form forward Joseph Tapine from Sunday's must-win clash against St George Illawarra.
Xavier Savage returns from an ankle injury for the Raiders at fullback, with Jordan Rapana moving to the wing while Albert Hopoate retains his spot on the other wing due to Nick Cotric's suspension.
The Dragons have included Tyrell Fuimaono and Billy Burns in their line-up in place of the suspended Tariq Sims and injured Francis Molo (ribs).
Newcastle have welcomed forward David Klemmer straight back into their team to play Brisbane, while Adam Clune replaces Jake Clifford in the halves.
The Broncos have named Te Maire Martin and Brenko Lee at fullback and centre respectively as Kevin Walters' team attempt to halt a two-game losing run.
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.
Connor Tracey is also absent due to concussion protocols but the Sharks welcome back Dale Finucane from suspension.
James Roberts comes back into the Tigers' lineup with Ken Maumalo (knee) out.
Roberts will play in the centres with Starford To'a taking Maumalo's spot on the wing.
The Warriors have moved Wayde Egan back to hooker with Daejarn Asi to partner Shaun Johnson in the halves for their clash with Canterbury in Auckland on Friday.
Tevita Pangai Junior will not travel across the Tasman due to family reasons with Raymond Faitala-Mariner to start at lock for the Bulldogs.
Centre Campbell Graham will miss South Sydney's clash with Parramatta as he remains sidelined with a cheekbone injury.
The Eels made one change from the team that beat Manly with Ofahiki Ogden coming onto the interchange in place of Makahesi Makatoa.
Aaron Booth's season-ending knee injury means Erin Clark moves back to hooker for Gold Coast for Sunday's game against Manly.
The Titans have kept Tanah Boyd at halfback with Toby Sexton named in the reserves.
The Sea Eagles have Josh Aloiai back from a knee injury on the bench while Kieran Foran has been named to face his future club despite coming off with a hamstring injury in last weekend's loss to the Eels.
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