He played for the Storm in Sunday's NRL final loss to Brisbane, but had been injured prior to that.
Coach Stacey Jones says Hughes will be missed, but his unavailability was expected.
Hughes' absence is off-set by 35-year-old Kieran Foran answering a halfback SOS before he retires.
Brisbane premiership winner Xavier Willison is the only uncapped player in the squad.
The Kiwi Ferns are boosted by the return of halfback Raecene McGregor from a 2024 sabbatical.
Warriors quartet Patricia Maliepo, Ivana Lauititi, Shakira Baker and Tysha Ikenasio have been selected for the first time, but Brisbane premiership winner Gayle Broughton is unavailable due to personal reasons.
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