The former Beatle said on his "Out There Japan Tour 2014" site that he wanted to perform Sunday against doctors' orders, but that his team wouldn't allow it.
"Unfortunately my condition has not improved overnight," he said. "I was really hoping that I'd be feeling better today. I'm so disappointed and sorry to be letting my fans down."
McCartney, 71, got sick Friday, and canceled his concert at the National Stadium in Tokyo at the last minute Saturday. But he had promised to be well enough to perform Sunday and do an additional concert Monday.
The tour site said McCartney instructed his team to look into rescheduling options. Ticket holders were advised to hold on to them, but where and when the concerts would be held was unclear.
Organizers said McCartney's scheduled performance was still on for Wednesday at Nippon Budokan hall in Tokyo, the same venue where the Beatles took the stage during their visit to Japan in 1966.
McCartney's tour continues to Yanmar Stadium Nagai in Osaka on Saturday, then to Seoul, before hitting several U.S. venues, including Dodger Stadium in Los Angeles.
McCartney said he was moved by the messages of concern and support he was receiving from his Japanese fans.
"I'm so very touched," he said.