Other charges relate to images of child sex abuse and obstruction of justice, said US attorney spokesman Joseph Fitzpatrick.
The 52-year-old Grammy Award-winning singer was already facing state charges of sex abuse towards four women in Illinois, three of whom were minors when the alleged offences occurred.
The arrest on Thursday night was carried out by New York Police detectives as well as investigators from the Department of Homeland Security, and it is expected that Kelly will be brought to New York to face the charges. Chicago police referred questions on the arrest to the US attorney’s office or New York police.
Kelly has denied the allegations and pleaded not guilty to the Illinois charges, and was released on bail.