"It's out of order," Tokyo governor Yoichi Masuzoe was quoted as saying by Kyodo News on Tuesday.
Masuzoe said he thought the city would have to pay far more than the 50 billion yen ($407.86 million) estimate, around a third of the overall cost for knocking down and rebuilding the facility, that sports minister Hakubun Shimomura had quoted.
Masuzoe was also unhappy with some of the items on the bill that Shimomura produced after a meeting with Prime Minister Shinzo Abe.
"We're asked to foot the bill for barrier-free design and air conditioning, but they are not going to be used solely for the Olympics," he said.
"If it's about this ridiculous figure that's been submitted to the prime minister's office, then he shouldn't bother coming over for an explanation."
Japan are looking to cut costs from the 170 billion yen bill because of budget-busting construction and rising labour costs.
Shimomura has scrapped the planned retractable roof and made around 35 percent of the seats at the 80,000 seat stadium, which will also host matches at the 2019 rugby World Cup, temporary ones in another cost-cutting measure.
Other venues for the Games, Japan's first since 1964, have also been hit by the budget cuts.
Tokyo will renege on its bid commitment to host a majority of events within 8 km (5 miles) of the Olympic village, with plans for 10 venues being looked into.
($1 = 122.5900 yen)
(Writing by Patrick Johnston in Singapore; editing by Amlan Chakraborty)
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