The 71-year-old singer was due to kick off his mini-tour in the capital Tokyo on Saturday, but he has fallen sick and doctors advised him to cancel the show, reported Daily Mirror.
McCartney rescheduled the postponed show for Monday.
"Thank you for such a beautiful and warm welcome to your country. I've unfortunately had to postpone tonight's show in Tokyo. I came down with a virus on Friday and following a visit from doctors, I've been told not to perform tonight," McCartney posted on twitter.
The Asian leg of his Out There! tour is due to continue in Osaka on May 24, before moving to South Korea.