The extra costs -- up 294 billion yen ($2.8 billion) from figures released a year ago -- come as officials work to build enthusiasm for the first Games postponed in peacetime.
A poll last week showed that a majority of Japanese oppose holding the Tokyo Games next year, favouring a further delay or outright cancellation of the massive event, and the latest budget could make the Tokyo Games the most expensive Summer Olympics in history.
Organisers, who have ruled out another delay and insist the Games can be held next year, defended the increased costs.
"Whether you see this budget as expensive or not depends on how you look at it," said Tokyo 2020 CEO Toshiro Muto.
"You can look at it from a cost perspective or an investment perspective. If you look at it purely in terms of cost, it doesn't make sense. But if you look at it as a positive investment, I think there are areas where it can be identified as such."
Organisers have tried to scale back elements of the Games in a bid to save money, scrapping athlete welcome ceremonies and scrimping on the all-important "look" of the event.
But these savings -- along with an expected 76 billion yen ($735 million) in extra revenue from sponsors and insurance payments -- have been outweighed by a plethora of extra costs, from rebooking venues and transport to retaining the huge organising committee staff.
Organisers increased the service budget of the Games to 731 billion yen ($7.1 billion), with extra money allotted for the opening and closing ceremonies, but the International Olympic Committee has agreed to cover the costs of moving the marathon and race-walking to northern Sapporo to beat Tokyo's summer heat.
A 96 billion yen ($929 million) budget will cover virus countermeasures, including the creation of an infection control centre in the Olympic Village -- part of a blueprint announced earlier this month along with plans to regularly test athletes and ban cheering in venues.
A study published earlier this year by Oxford University warned that the Tokyo Games could become the most expensive Summer Olympics ever.
The study calculated that the 2012 London Games was the most costly to date, with a $14.96 billion price tag eclipsed only by the eye-watering $21.89 billion spent on the Sochi Winter Games in 2014.
