The embattled utility at the centre of the worst nuclear accident in a generation said its year-to-March shortfall came in at 685.3 billion yen, smaller than a year-earlier loss of 781.6 billion yen.
But the latest figures were worse than a previous 120 billion yen loss estimate that TEPCO, or Tokyo Electric Power, announced just two months ago.
The company said the massive loss was mainly due to growing compensation as it booked 1.16 trillion yen in extraordinary losses related to expected damages for nuclear accident victims.
It also said the recent fall in the yen boosted energy expenses, already high after being forced to turn to pricey fossil fuels in the absence of a nuclear alternative.
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TEPCO declined to announce its forecast for the current fiscal year, only saying it would "make an announcement without any delay when we are in a position to forecast results".
A 9.0-magnitude tremor struck off Japan's northeast coast in March 2011, triggering monster waves that swamped the Fukushima plant's cooling systems, sparking reactor meltdowns and radiation leaks.
In April, the Fukushima plant suffered a series of radioactive water leaks, the latest in an increasingly long line of mishaps to rattle public confidence.
Two years since the worst nuclear accident in a generation, the plant remains fragile, with systems to cool spent nuclear fuel failing repeatedly in a matter of weeks in March and April.