Cal Crutchlow joined fellow MotoGP riders Ben Spies and Hector Barbera on the sick list at Motegi.
Spies suffered food poisoning on his way to Japan, while Barbera and now Crutchlow have 'flu like symptoms.
Monster Yamaha Tech 3 rookie Crutchlow will start his first Japanese Grand Prix from twelfth on the grid.
“I'm a bit disappointed to be back in twelfth when you look how close I am to the third row. But I can't be too upset because I feel well below my physical best today," said the Englishman.
"All last night I was coughing and sneezing and I've been drinking about eight litres of water today and I still feel dehydrated. My throat feels like I've swallowed gravel but I still managed to go out there and lap faster than last year's pole time.
"I can't really ask for much more than that on a circuit I've never even seen before in my life."
Barbera, who like Spies was feeling a bit better on Saturday, qualified as the top satellite bike rider in ninth.
Although not sick, Crutchlow's fellow rookie Karel Abraham continues to struggle with the after-effects of a big knock to the head at Aragon.