The sex acts are alleged to have occurred between May 1998 and January 2010, according to prosecutors
R Kelly has been arrested on child pornography and other charges, the New York Times reported, in the latest criminal investigation into the R&B superstar dogged by allegations of sexual misconduct.
The 52-year-old, whose legal name is Robert Kelly, was taken into custody by federal agents in Chicago late Thursday, the newspaper said.
Federal prosecutors have issued a 13-count indictment against the singer, which also includes enticement of a minor and obstruction of justice charges, assistant US attorney Joseph Fitzpatrick told the Times.
Kelly has a decades-long history of abuse allegations, especially of underage girls, and was acquitted in a child porn trial over a decade ago.
In 1994 he wed his protege Aaliyah, the late R&B star who was 15 at the time.
Kelly, then 27, had produced the teenage singer's debut album titled "Age Ain't Nothing But a Number." Their marriage was later annulled, and Aaliyah died in a plane crash in 2001.
Despite unsettling claims against him, the decorated musician - known for hits including "I Believe I Can Fly" - has continued to perform and maintain a solid fan base.
But his fortunes began to shift after the January release of a six-part documentary called "Surviving R Kelly."
The documentary, which alleged that Kelly engaged in sexual, mental and physical abuse of girls and women, prompted Chicago prosecutors to publicly seek out potential victims.
Prior to Thursday's arrest, Kelly was on bail for a slate of charges in Chicago, including five felony counts of aggravated criminal sexual assault.
He spent three nights behind bars and was released after coming up with $100,000, 10 percent of the $1 million bail set in court.
The sex acts are alleged to have occurred between May 1998 and January 2010, according to prosecutors.
If convicted of the most serious charges in that case, Kelly would face mandatory sentences of six to 30 years in prison on each count.
In a March interview, Kelly vehemently denied the charges and said he was "fighting" for his life.
"I didn't do this stuff," he told CBS News.
"Whether they're old rumors, new rumors, future rumors, not true," added Kelly, who became upset and emotional during the interview.
He denied a report by BuzzFeed in 2017 that said he had kept women as virtual sex slaves at homes he owns in Chicago and Atlanta.
Kelly was also briefly detained in March for failing to pay $161,000 in child support payments he owed to his ex-wife and their three children.