Western Japan last week was hit by the strongest typhoon to strike the nation in 25 years, and then just days later by an earthquake that paralysed the northernmost main island of Hokkaido and left roughly 40 dead.
Japan also suffered through a summer of record-breaking heat and deadly, torrential rains in July that unleashed landslides and flooding.
Coates, who is chairman of the Coordination Commission for Tokyo 2020, admitted that the two disasters just a week before had been a bit of a reality check about the planning difficulties for what are already extremely complex Games due to the largest number of sports and events ever.
"So what happened last week and what happened in Osaka certainly have hit home to me, and I know the Organising Committee, about the further complexity of planning these games," Coates told a news conference, referring to a storm surge that submerged Kansai International Airport just off the western city of Osaka.
He said he knew organisers were taking the issue seriously and factoring it into their planning and scheduling.
"In Sydney, we had a simulation exercise one week of what could go wrong, but they were all disasters that we dreamt up: a train coming off the rails out in the Blue Mountains, someone bursting through and attacking one of the marathon runners. Those sorts of things," he added.
"But you don't have to dream anything up in this country, it's very sad to say."
Coates, who was in Tokyo for a two-day IOC project review meeting, said he was pleased with how things were shaping up, including deciding the last piece of event scheduling, that of swimming.
The finals will be held in the morning and the heats in the evenings - a schedule that had been widely expected but drew protests from the Japanese Swimming Federation (JSF) in July, which expressed disappointment that local television viewers will not be able to watch finals in a prime-time slot.
Tokyo 2020 later said in a statement that swimming events will be held for nine days from July 25, with all heats being held in the evening and finals taking place the following morning.
(Reporting by Elaine Lies; editing by Sudipto Ganguly)
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