Nakamura, whose left-foot kicks helped Celtic to their third straight Scottish Premier League title, was feeling recurring pain from an old injury to his right ankle, according to Japanese press reports.
He jogged and had a light workout without his boots at Japan's training camp in Bangkok on Tuesday with the painful ankle taped.
"The pain usually goes away in a couple of days. But the ankle still hurts even if it's taped," the 30 year old told Japanese reporters.
"I'll try to be alright for the Thailand match."
Japan coach Takeshi Okada said of Nakamura: "He didn't want to strain himself as the pain had not subsided. I must think about the worst case in which it is impossible for him to play."
The pain came back after a 1-1 away draw with Oman on Saturday, which put Japan closer to a berth in the final Asian qualifying round.