Chan is the form men's figure skater on the planet at present having set world records in the short, free and combined at the Trophee Eric Bompard is Paris last month.
However the three-time world champion saw the first of those stripped from him in Fukuoka as Hanyu scored 99.84 points for his short program, bettering Chan's mark of 98.52.
That was enough to put the Japanese skater into the lead with Chan only scoring 87.47 after touching the ice on the landing of his triple axel and doubling a planned triple lutz.
And it was double success for Japan on the opening day of the Grand Prix Final as Olympic silver medallist Mao Asada skated into the lead after the ladies short program, scoring 72.36 points.
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