The parents of the 23-year-old petitioned the government this year to recognise his suicide as "karoshi" - or "death by overwork", with media saying he had worked 200 hours of overtime a month before his death.
"To our regret, illegal overtime was recognised as a result of inspection by the labour ministry," said Tadashi Mochizuki, director of stadium manager the Japan Sport Council (JSC), which is part of a joint venture with construction firm Taisei Corp.
"We, JSC and Taisei, took it sincerely and we'll do the utmost (to comply with the law) in proceeding with construction."
Authorities unveiled a model of the new stadium in the Japanese capital, which is set to be completed in November 2019, after construction begun in December 2016.
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Japan's fast-ageing society has left employers grappling with an acute labour shortage. It officially recognises two types of "karoshi": cardiovascular illness linked to overwork, and suicide following mental stress related to work.
Employers face few curbs on overtime and pay, so that more than a fifth of company staff exceeded a government overtime threshold of 80 hours a month, a white paper showed in 2016.
The trend was spotlighted by a high-profile death from overwork in 2015 at advertising giant Dentsu Inc. Last week, public broadcaster NHK said a 31-year-old reporter died four years ago of overwork.
To tackle the problem, the government plans sweeping reforms of job practices, including overtime caps and better pay for part-time and contract workers.
(Writing by Tetsushi Kajimoto; Editing by Clarence Fernandez)
