The defending two-time champion, who leads the standings after three races, was admitted to hospital in nearby Kumamoto on Friday after suffering chest pain, coughing and shortness of breath.
He was diagnosed with pneumothorax, a collapsed lung, and will skip this weekend's fourth round of the season to focus on his recovery.
Nojiri commented: "I'm sorry that I won't be able to participate in this race. I will concentrate on my treatment and do my best to prepare for the race so that I can race in front of everyone again in the best possible condition."
Mugen team director Hirokatsu Tanaka said that Nojiri had only been in pain from Friday, and doesn't expect him to have a long lay-off.
"It's not something that requires surgery, so I don't think [his recovery] will take that long," Tanaka told Autosport's Japanese edition jp.motorsport.com. "But at least for today and tomorrow, as expected he is taking care of himself and is absent."
Honda reserve driver Hiroki Otsu will step in to replace Nojiri at the Mugen squad alongside Liam Lawson.
Source: Autosport