The Japanese engineering conglomerate said the unnamed employee had "overstated numbers and made misstatements" in what it described as "inappropriate" accounting at Toshiba Medical Information Systems.
The false accounting happened over a six-year period starting in 2006, the conglomerate said, adding that it inflated the division's profits by about USD 100 million in total.
In response, a manager who ordered his underling to fake the financial statements was fired while the unit's chief executive and directors have agreed to step down, Toshiba said.
However, the vast company said it did not expect the scheme which saw profits inflated by USD 100 million to "materially affect its consolidated financial results for the past fiscal years".
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The revelation came as Toshiba said its net profit for the six months to September fell 14.4 per cent to USD 218 million due to a tax change.
Operating profit soared 53.7 per cent to 105.6 billion yen on sales of 3.04 trillion yen, up 13.2 per cent, it added, crediting strong sales of electronic devices and memory chips.