McGillvary will not be considered for the Test match in Perpignan.
England coach Shaun Wane, who held his first training session on Tuesday, has also ruled out Warrington hooker Daryl Clark and Warrington stand-off George Williams (shoulder) – now back in Super League after a spell in the NRL with Canberra – due to injury.
“It’s been a tough year and the games have come thick and fast so I knew it was coming,” Wane said.
“The players are smashed up. For Daryl Clark to play the last match with two fractured ribs and torn medial ligament in his knee shows the toughness of the players we have in our sport.”
Wane remains confident in the strength of his squad and says the injuries will pave the way for several fringe players to get their chance.
“We trained this morning and we had 10 young kids from the England Knights in and they acquitted themselves really well,” he added on Tuesday.
“With McGillvary missing, it’s a chance for example for Liam Marshall to step up.
Wigan have appointed assistant Matt Peet as their new head coach and brought Shaun Wane back to the club.
The club also sprung a surprise with the appointment of former Warrington player and assistant coach Lee Briers to their new-look backroom team.
Peet has replaced Australian Adrian Lam, whose three-year reign was brought to a halt at the end of the 2021 season and, at 37, becomes the youngest head coach in Super League.
His assistants will be Briers and Sean O’Loughlin.
Wane will combine his role as England head coach with that of leadership and management director of the Warriors.