Dupont was a key part of the Toulouse squad that wrapped up a fourth consecutive Top 14 title with victory over Montpellier on Saturday.
Already unavailable for the opening Nations Championship match against New Zealand on July 4, the federation said the scrum-half will now also miss games against Australia on 11 July and Japan a week later.
Dupont will be replaced in the squad by Toulouse teammate Paul Graou.
The two other scrum-halves included in the squad are tour captain Maxime Lucu of Champions Cup winners Bordeaux-Begles and Racing 92's Nolann Le Garrec.
There was no reason given as to why Dupont would not make the trip, but bi-weekly rugby newspaper Midi Olympique said he was carrying a calf injury.
The Nations Championship is the inaugural competition that pitches teams from the northern hemisphere against their southern counterparts.
After six rounds, three each in July and November, the competition will climax with six matches at Twickenham in late November to determine final placings.
Dupont's absence is a blow for a player who had been hoping to make a first summer tour with France since 2017, with senior players often rested.
It also comes just a year out from the Rugby World Cup in Australia.
Dupont has enjoyed a stop-start season, returning from a serious knee ligament injury sustained against Ireland in the 2025 Six Nations only in late November.
After a lukewarm 2026 Six Nations, Dupont then picked up a groin injury that saw him reduced to being a spectator for a spell.
But he was back to his imperious best as the domestic season ended, shining for Toulouse in their 71-17 Top 14 semi-final demolition of Racing 92.
He was substituted off in the 64th minute of Saturday's final, which Toulouse won 28-20, not seemingly in any apparent discomfort.
Dupont even reappeared late in the game as a replacement for fly-half Romain Ntamack.
Dupont was to be one of nine players from the Top 14 final called up to the France squad, including six from Toulouse: Ntamack, hooker Peato Mauvaka, lock Emmanuel Meafou, back-rower Alexandre Roumat and centre Kalvin Gourgues.
Three Montpellier players were also selected: back-rower Lenni Nouchi, lock Florian Verhaeghe, and centre Auguste Cadot.