The criminal charges were filed under seal in the US District Court for the Eastern District of New York, the report said on Tuesday.
Santos could reportedly appear in court as soon as Wednesday.
Although the exact nature of the charges remain unknown, investigators have been probing allegations of false statements in Santos’ campaign finance filings.
In late December last year, Santos revealed he had misrepresented his background, education and employment history on his CV. The confession came after US media published an investigation pointing out inconsistencies in his biography.
One was the claim that he worked for investment bank Goldman Sachs. The company denied this, with Santos stating in his defence that he worked for a firm that had a limited partnership with one of the world's largest investment banks. The media also reported Santos had allegedly set up a fraudulent credit card skimming scheme in 2017.
Later, speaking to reporters in Washington, Santos was asked if he was going to resign amid discontent among his fellow party members. The congressman replied that he had no intention of leaving office.
Last month, Santos also announced his candidacy for reelection in 2024.