FIFA President Gianni Infantino, who is seeking re-election, has faced opposition since his failed move in July to bring private investors into a new FIFA commercial entity holding rights linked to competitions including the World Cup.
"I am grateful that I can make this announcement with the full support of the JFA," Tashima said.
"It's not about winning or losing but about conveying to the world the honest, sound and upright attitude that Japanese football has built. What FIFA needs now are these values that we have protected. I have decided to run in order to make this appeal to the world."
Reuters has contacted the JFA for comment.