"We are cooperating with investigators and take those probes seriously", a Facebook spokesman told the Times in a statement.
The investigation is being overseen by United States attorney's office for the Eastern District of New York, and a grand jury has been convened, The NY Times reports that the focus of the investigation remains unclear for now.
In addition to looking at the data deals, the probes focus on disclosures that the company shared the user data of 87 million people with Cambridge Analytica, a British consulting firm that worked with U.S. President Donald Trump's campaign.
As if today couldn't get any worse for Facebook, the company is now facing a criminal investigation as the result of its controversial data sharing practices.
The US Justice Department's fraud unit is also investigating the Cambridge Analytica scandal. The deals helped Facebook gain more users, according to the report, and its partners were able to access user data without obtaining consent.
Facebook has defended the deals.
The Times reports that a NY grand jury subpoenaed two unidentified smartphone makers who are involved in data partnerships with Facebook allowing them access to the social network's two billion users.
The deals sparked outrage - and have come under sharp scrutiny - since they were revealed in a investigation by the Times past year.
Facebook did not immediately respond to a request for comment.
Facebook has spent the last two years eliminating those partnerships, the Times added.
Facebook is already facing the prospect of multi-billion dollar fines to settle privacy investigations by the US Federal Trade Commission and other agencies.