The storm is shifting its course from the Tokyo area to northeastern regions, including Fukushima. But the agency warned of heavy rain, wind and high waves over a wide area including the capital.
"In line with the current weather forecast, the schedule for the rowing and archery events due to take place on the 27th have already been changed," Tokyo 2020 said.
"At this time, there are no plans to change the schedule for any of the other events due to be held on Tuesday."
The Games organisers said they would keep a close eye on the forecast and activate contingency plans for bad weather "should the need arise".
Meanwhile Olympic surfing chiefs decided to take advantage of big waves whipped up by the storm at Tsurigasaki Beach, 100 kilometres (60 miles) east of Tokyo by scrapping the final day of competition. Medal events will now be crammed into Tuesday's schedule.
Evacuation orders were issued in the area surrounding the resort town of Atami, which was hit by a devastating landslide earlier this month that killed 21 people, with six still missing.
Some train services, including bullet trains, will be suspended on Tuesday afternoon because of the storm. The meterological agency also referred to Nepartak as a typhoon, while the US Navy called it a tropical storm.
Japan's typhoon season runs from around May to October, peaking in August and September.
In 2019, Typhoon Hagibis hit as Japan hosted the Rugby World Cup. The powerful storm killed more than 100 people, and forced organisers to cancel three pool matches.
The Olympics opened on Friday after a year-long pandemic delay and will run until 8 August. Spectators are banned at most venues because of coronavirus risks.