The 52-year-old Kelly was denied bail in a Brooklyn courtroom packed with his supporters.
He appeared sullen as prosecutors told Magistrate Judge Steven Tiscione he posed a flight risk and a danger to public safety.
Kelly's defense attorneys requested his release so he could better fight charges they have dismissed as "groupie remorse."
Kelly, whose full name is Robert Kelly, is accused of using his fame to recruit young women and girls into having illegal sexual activity. Prosecutors say he isolated them from friends and family and demanded they call him "Daddy."
Friday's hearing followed Kelly's arrest last month in a separate Chicago case accusing him of engaging in child pornography.
Kelly is charged in New York with exploiting five victims, identified only as "Jane Does." According to court papers, they include one he met at one of his concerts and another at a radio station where she was an intern.
Prosecutors allege Kelly arranged for some victims to meet him on the road for illegal sex. He had one victim travel in 2017 to a show on Long Island, New York, where he had unprotected sex with her without telling her "he had contracted an infectious venereal disease" in violation of New York law, they say.
Kelly's attorneys said in court filings the alleged victims sought out Kelly's attention, came to his shows and "pined to be with him."
Kelly "would spend his time and even become friends with and care about these groupies and fans who were dying to be with him," they added.