The 25-year-old will skip the event for the second year in succession after suffering a leg injury in 2025.
"On arrival in Europe, the fracture close to his left thumb has been found to require surgery which he will undergo on Thursday," Trackhouse said in a post on Instagram.
Ogura's absence is a setback for the Japanese rider, who claimed his maiden MotoGP victory at the Dutch Grand Prix in Assen in June and sits third in the riders' standings.
Ogura trails championship leader Jorge Martin of Aprilia by 37 points ahead of the August 28-30 race at Aragon.
Trackhouse said Italian test rider Lorenzo Savadori would replace Ogura for the Spanish Grand Prix weekend.