The 24-year-old had been called up by Sarina Wiegman for the Lionesses opening Nations League clashes, as England prepare to meet Scotland and the Netherlands in League A Group 1.
However, Wubben-Moy is understood to have suffered a small muscular problem, and she will remain in North London to undergo treatment rather than represent her country this month.
With the centre-back out of contention, Aston Villa's Lucy Parker has taken her place and will be bidding to make her debut for the Lionesses during their pair of Nations League contests.
Wubben-Moy, meanwhile, has earned 10 caps for England and made Wiegman's 2023 World Cup squad, but she did not play a single minute during the Lionesses' run to the final.
Wubben-Moy's Arsenal teammate Beth Mead is already out of the squad owing to her ACL injury, while Fran Kirby, Keira Walsh and Bethany England are also absent, and Alessia Russo will be a late arrival to the camp on Wednesday.
The Lionesses play their inaugural Nations League match against Scotland at the Stadium of Light on Friday before taking on the Netherlands at the Stadion Galgenwaard in Utrecht four days later.
Meanwhile, Arsenal - who have already been knocked out of the Women's Champions League in qualifying - will open their 2023-24 Women's Super League season against Liverpool at the Emirates on October 1.