The Italian veteran has been struggling with injury since damaging his shoulder joint and fracturing ribs in a crash at Assen last month.
However, the Pramac Ducati man will ride through the pain in the Czech GP at Brno this weekend.
“Unfortunately, the shoulder problem is persisting,” he said.
“The doctor said I should undergo surgery, but I’ll only consider that after the championship. For now, I’m undergoing therapy every day.
“For Brno, I hope to continue improving my physical condition. I’ve rested during this two-week break, which I really needed.”
Pramac Racing technical director Fabiano Sterlacchini said: “Loris Capirossi…certainly won’t be at 100 per cent.”
“Loris continues to undergo daily therapy on his shoulder. After the miracle at Laguna Seca, where he managed to finish the race, there’s hope that he’ll be better.”