The Mayor of London who is in the country on a trade visit was invited to join children on a mini turf pitch in Tokyo for the non-contact game.
Toki Sekiguchi was knocked to the ground and said he "felt a little pain".
The mayor, a keen rugby fan, shook the boy's hand and apologised.
In the game of touch rugby the person with the ball is stopped by being touched, not tackled, as in union rugby.
Slo-mo BoJo
He has form. He brought a child to the ground last year in a football kickabout.
And in 2006 he played in a charity England-Germany football match. Although only on for 10 minutes he stunned the 20,000-strong crowd by flooring retired German midfielder Maurizio Gaudino in a rugby-style tackle.
Of that incident he said: "When he was about two yards away I just put my head down. I was going for the ball with my head, which I understand is a legitimate move in soccer."
In Tokyo, the pair later posed for photographs and Mr Johnson handed over a 2015 rugby ball to the youngster.
Boris Johnson has knocked over a 10-year-old child while playing touch rugby in Japan.