The parent company of Atlas is being investigated in Japan for "shady practices," according to this Kotaku report. In Japan "Atlus" is just a brand on paper and not a real company anymore because the Japanese company was dissolved and delisted from the stock market a few years ago after it became a wholly owned subsidiary of a company called Index.
That company is now being investigated by Japanese authorities for questionable bookkeeping. Japanese authorities are sifting through the company's books and are also conducting an investigation at the home of the company's president, according to Kotaku (citing a report from NHK). The company is specifically being investigated for an illegal business practice called "round-tripping," or fabricating and inflating business transactions to beef up a company's balance sheet. In America we might calling it "cooking the books."
"It's true that we are being investigated," an Index spokesperson told NHK. "During this investigation, we are unable to divulge any information at the request of the authorities. From here on out, we are cooperating fully and as soon as all the facts are evident, we will promptly make that known."
The investigation likely won't have any short term affect on Atlus in America. The company will continue to bring wonderful RPGs from Japan to America for the foreseeable future.