Hiroshima-based Urban failed last week, facing debts of around $2.35 billion - the largest bankruptcy declared in Japan since 2002.
The firm's collapse occurred on the same day in which it said that it had been performing derivative transactions which returned funds to its banker BNP Paribas.
This is despite Urban's announcement two months ago that it was merely selling $273 million of convertible bonds to the French bank - with no mention of the derivative transactions.
Marc Goldstein at Institutional Shareholder Services told the news agency that this demonstrates a "lack of transparency" - and termed Urban shareholders "victimsâ¦of the company".
The Tokyo exchange appears to agree, with spokesman Satoshi Futagi announcing the investigation by saying that the August 13th disclosure of the derivatives transaction was "unsuitable".
For its part, Urban said that it was currently discussing the matter with the exchange.