The bank agreed last July to pay $410 million to settle the case. While Masters was not cited for wrongdoing, her name appeared in the regulator's order a number of times.
It is not immediately clear what the Manhattan prosecutors are investigating.
JPMorgan was not immediately available for comment outside regular U.S. business hours.
Masters, who began her career at the bank with an internship in London, wanted to continue as the chief of the commodities business even after its sale to Geneva-based Mercuria Energy Group, Bloomberg said.
JPMorgan is selling its physical commodities to Mercuria for $3.5 billion and Masters is expected to leave the bank in a few months after assisting with the sale.