Dubi said Tokyo had abandoned plans to build a new basketball venue and would instead hold matches in an existing venue that was used for the world championships.
Dressage and show jumping are now to be held in the venue that hosted those events in the 1964 Olympics, while the canoe slalom is to be moved "a few hundred metres" because of environmental concerns over the original location.
"At this point in time it is close to a billion (in savings) compared to the revised budget so it is a very substantial figure and it will continue to grow," Dubi said after the Tokyo 2020 organisers presented their plans to the International Olympic Committee's executive board meeting in Rio de Janeiro.
Other venues might change, Dubi said, and Tokyo will present a fully revised plan by April with the intention of locking in all changes for final approval by the IOC's executive committee in June.
The announcement came just a day after planners for the Tokyo 2020 Summer Olympics issued their playbook for organising the sports extravaganza.
Rising labour and construction costs have forced Tokyo to rethink its plans for 10 venues it intended to build for the Games, reneging on a bid commitment to host a majority of events within 8 km (5 miles) of the Olympic village.
That did not perturb Dubi, who said there was enough time to make the moves and still ensure the athletes were not unduly affected.
"We are still in the timeframe where you can confidently make these changes," Dubi told reporters.
"The athletes' experience remains what it was in the bid. That was what was promised. But to change at this point in time especially when you are using existing venues is something that is largely feasible."
Planners allotted $1.5 billion for venues in Tokyo's Olympics bid but that estimate more than doubled late last year after a recalculation.
The city won the Games over Madrid and Istanbul by emphasising Japan's organisational prowess and $4.5 billion in the bank.
(Additional reporting by Elaine Lies in Tokyo, editing by Nick Mulvenney)
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