Matt Kallman, a spokesman for Uber, said the company is cooperating with the investigation, and the Hell program is no longer being used.
Representatives for the FBI and Acting US Attorney Joon Kim in Manhattan declined to comment on the probe.
Lyft drivers filed a class-action lawsuit against Uber over the Hell program in San Francisco federal court in April.
A judge granted Uber's request to dismiss the case last month, but allowed it to be revised and refiled. News of the New York investigation into Uber's practices was reported earlier by The Wall Street Journal.
Closely-held Uber has been beset by legal and regulatory scrutiny across a range of its practices, contributing to the pressure that ultimately resulted in the resignation of co-founder and former Chief Executive Officer Travis Kalanick in June. Major early-stage investors in Uber rebelled against Kalanick's leadership after a string of controversies, including its treatment of female employees and drivers.
Uber hired Dara Khosrowshahi, who was chief executive of travel website Expedia, to take over the helm of the ride-sharing service beginning this week. Khosrowshahi has said he plans to draft a new set of core values for the company and hopes to clean up its troubles to ready it for a public offering, possibly in 2019.