TOKYO—Japan's financial regulator said Friday it has halted operations of a little-known Tokyo money-management company after the firm allegedly lost billions of dollars in client money.

In one of the biggest cases of its kind in Japan, with Tokyo's reputation as a financial center still bruised by the billion-dollar Olympus Corp. accounting scandal, the regulator said investigators found that AIJ Investment Advisors Co. can't account for "most of" the 183 billion yen, or about $2.3 billion, in pension-fund assets under management.

The money belongs to a mostly unidentified range of Japanese companies. Microchip-testing-equipment maker Advantest Corp. and industrial-robot maker Yaskawa Electric Corp. have confirmed that they placed pension money with AIJ.

Underlining the gravity of the case, Financial Services Minister Shozaburo Jimi said at a news conference in the capital that the regulator, the Financial Services Agency, will now scrutinize operations at all 263 investment-management firms in Japan because of the AIJ investigation.

The FSA said securities investigators have been probing 120 cases involving AIJ clients since January. But officials said that with the investigation ongoing, they couldn't comment on details, including why the money was missing or the exact amount of losses. The agency has ordered the firm to suspend operations for a month.