Japan chose the new design by a Japanese architect on Tuesday after Hadid's stadium plan set off a row over a $2 billion price tag that would have made it the world's most expensive sports venue.
"Sadly the Japanese authorities, with the support of some of those from our own profession in Japan, have colluded to close the doors on the project to the world," Hadid said in a statement released by her firm.
"This shocking treatment of an international design and engineering team ... was not about design or budget," she said.
"In fact much of our two years of detailed design work and the cost savings we recommended have been validated by the remarkable similarities of our original detailed stadium layout and our seating bowl configuration with those of the design announced today," she added.
Tokyo's preparations for the global games suffered a humiliating setback this year when the government pulled the plug on her plan following spiralling costs and complaints over the design.
Two new plans -- both by Japanese architects and with sharply lower cost estimates -- were released last week by the Japan Sport Council, which is overseeing the project.
After deliberations, the JSC chose the slightly cheaper of the two, a joint venture involving renowned architect Kengo Kuma with an estimated cost of approximately 149.0 billion yen ($1.2 billion).
Under the new plan, construction is to be completed in November 2019, ahead of the January 2020 deadline demanded by the International Olympic Committee.
Tokyo is due to host the opening ceremony on July 24 that year.
The new plan, which calls for five floors above ground and two below, involves placing greenery on stadium decks to shut out Tokyo's scorching summer sunshine. Seating capacity will be about 68,000.
