The stock opened down more than 13 percent. It later recovered some of those losses, but still ended the day more than 8 percent lower.
In a regulatory filing Friday, the food company said the SEC issued a subpoena "seeking relevant documents" following a delay of the company's earnings report.
The company said it is in the process of responding to the agency's request and intends to cooperate fully.
Hain contacted the SEC in August to advise it about the delay in filing the quarterly report and about an independent review by an audit committee, according to the filing.
In November, the company said it found no evidence of intentional wrongdoing in connection with its financial statements.
The stock is down more than 1 percent in the past year.