Tokyo Electric Power Co reported a net loss of $15bn (£9bn) to account for the disaster at its Fukushima nuclear power plant and it warned its future was uncertain.
The company said President Masataka Shimizu, 66, will step down to take responsibility for the disaster and radiation leaks at the plant, making way for an insider, managing director Toshio Nishizawa, 60.
The company's loss was the country's biggest outside the financial sector.
Engineers are battling to bring the plant under control more than two months after a 9.0 magnitude earthquake and deadly tsunami led to the worst nuclear crisis since Chernobyl.
The disaster has triggered a drop of more than 80 per cent in Tokyo Electric's share price and prompted the government to step in with a fund to handle compensation claims that some analysts say could top $100bn. The results were released after the close of trading.
Shimizu, speaking to a packed news conference at its headquarters in Tokyo, bowed at the start of the press conference. Nishizawa, who has worked at the utility since 1975, stood to his left.
"We feel sorry for the victims of the earthquake and tsunami. At the same time we want to sincerely apologise for our nuclear reactors in Fukushima causing so much anxiety, worry and trouble to society," the outgoing president said.
For the business year that ended 31 March, the company, commonly known as Tepco, posted a 1.25 trillion yen net loss after accounting for the 1 trillion yen cost of scrapping reactors at the Fukushima complex and writing off tax assets.
Shimizu did not make any public appearances in the two weeks that followed the 11 March disaster, sparking criticism that the company lacked leadership as it fought to bring the plant under control. Shortly after, he was hospitalized with dizzy spells as Tepco's share price plummeted and the company lurched close to collapse.
City A.M. Reporter