The former Beatle got a virus last week and canceled several concerts, apologizing online to fans.
Now, his organizers say he is not well enough to do any of the concerts in Japan, including the one set for Wednesday at Nippon Budokan hall, where the Beatles performed during their first Japan tour in 1966.
The official site of McCartney's "Out There Japan Tour 2014" said his doctors are ordering him "complete rest."
McCartney, 71, is still scheduled for a concert in Seoul, South Korea, on May 28 at Jamsil Sports Complex Main Stadium, followed by 19 U.S. performances.
In Japan, two weekend concerts in Tokyo, a makeup concert scheduled for Monday and another in Osaka on Saturday were all canceled.
Representatives for McCartney declined further comment Wednesday about his illness.
Tickets are being refunded from Thursday. The most expensive tickets cost 100,000 yen ($1,000) each. Some fans traveled from out of town for the concerts. Japanese are among the world's most avid followers of Western pop music.
Yohei Hashimoto, 52, said he traveled from western Japan for multiple concerts that were cancelled. "Well, what can I do about it? I would rather wish for Paul McCartney to get better sooner and come back to Japan again," he said.
"I'd like to thank my Japanese fans for their love, messages of support and understanding," McCartney said in a statement. "I hope to see you all again soon. Love, Paul."
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