In a statement on the Skating Japan website, the Japanese star primarily cited concerns over his asthma and how he would be affected were he to contract COVID-19.
He said, "There is still no conclusive evidence about the relationship between bronchial asthma and COVID-19 so it’s difficult to make a judgement. But there is information that those with asthma contracting COVID-19 will make the condition worse so I need to be as cautious as possible.
"I believe we should not create opportunities to spread the infection. If my withdrawal can help protect against the spread of infection, it may become one action which will contribute to stopping the spread of infection.
"It is with deep regret that I have decided to withdraw from this season's ISU Grand Prix series. I hope for the end of the COVID-19 pandemic as soon as possible." - Hanyu Yuzuru
Hanyu, who is currently in his homeland, also highlighted the logistical issues of his Toronto-based coach Brian Orser attending the Grand Prix event in Japan, saying Orser's absence would mean he cannot compete in "perfect form".
And for the 25-year-old to compete at Skate Canada, he would need to self-isolate for two weeks after flying in from Japan.
After cancelling the Junior Grand Prix, the ISU announced three weeks ago that the senior series would take place with events featuring competitors from the host country, those who train regularly in the host country, and competitors from "respective geographical areas" if they are able to travel safely and legally.
The ISU also committed to hosting December's Grand Prix Final in Beijing, a test event for the Beijing 2022 Winter Olympics.
With each skater allowed to compete just once in the series, that left Hanyu with a potential choice between Skate Canada in Ottawa at the end of October and late November's NHK Trophy in Osaka.
But this decision to skip the entire event means the sport will be missing its most popular athlete for at least the next few months.