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.
Otsu previously drove for the team in 2021, winning a race at Motegi, and raced for the Dandelion Racing team last year.
He lost his seat to rookie Kakunoshin Ota for the 2023 campaign, but stepped in for the Suzuka pre-season test in March when Ota suffered an injury in a crash in SUPER GT pre-season testing.
Tanaka added: "Otsu took part in the pre-season test, but it's hard to say how well he can do until he actually drives.
"But when he raced for Mugen, he won a race at Motegi, and he knows the car, so I think we can expect him to be fighting towards the front. I want him to give it his best with that target in mind."
Nojiri currently holds a four-point championship lead over TOM'S driver Ritomo Miyata in the standings, with Lawson third, seven off the lead.
Additional reporting by Kenichiro Ebii
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