The company’s spokesperson said it is the first loss of its kind in Mitsubishi's history.
It may be the biggest loss in the oil markets since China's Sinopec Corp said last year it lost about $700 million on crude hedging.
The trader who carried out a series of unauthorised transactions disappeared in August.
While trying to locate the trader who had not returned to its Petro-Diamond Singapore (PDS) oil unit after a holiday, Mitsubishi discovered the losses.
The employee was discovered to have been repeatedly engaging in unauthorised derivatives transactions and disguising them as hedge transactions since January 2019, he said, adding that the issue has been reported to police and the trader's contract was terminated.
The spokesperson could not say what the impact on the trading house's earnings would be. Its profit surpassed $5 billion in the year through March 2019.
Founded in 1954, Mitsubishi has a reputation as a careful trader and only reported its first annual loss in 2016 when commodities markets slumped.