The bank is pursuing 35.2 billion yen ($352 million) in losses it believes were incurred through loans via Marubeni to medical company Asclepius, which has since gone bankrupt.
An elaborate hoax featuring forged documents was allegedly conducted by Marubeni employees, according to the Wall Street Journal.
Matthew Russell, head of corporate communications at Lehman Brothers, said that they were "working closely with Japanese authorities" in an investigation of the fraud.
"We are confident in our legal claim which we will pursue until we receive repayment from Marubeni," said Mr Russell.
Marubeni distanced itself in a statement from the fraud and stated it had "no obligation to cover any repayment requests".