The singer's crisis manager, Darrell Johnson, says his legal team was expecting the indictment to happen but he doesn't know what the charges are yet.
Prosecutors said Kelly and his entourage recruited women and girls at concerts and other venues to "engage in illegal sexual activity".
Chicago prosecutors alleged in their 13-count indictment that Kelly had sexual contact with five minors, recorded videos of some of them and paid them off to buy their silence.
Joseph Fitzpatrick, a spokesman for the U.S. Attorney's Office, confirmed to the Associated Press that authorities took Kelly, 52, into custody Thursday evening.
The indictment in the Northern District of IL contains allegations of child pornography and obstruction of justice.
"He's expected to be arraigned today in federal court in Chicago and at a later date in Brooklyn", the source added.
An attorney for the 52-year-old Grammy Award victor says Kelly denies wrongdoing. CBS News correspondent Jericka Duncan reports this is the first time Kelly has faced federal criminal charges.
"This is a very positive day for those who allege that they are victims of Mr. Kelly, and it is a day that I'm sure that Mr. Kelly hoped would never come", she said. The investigation could also include child pornography.
Kelly has been the subject of allegations of sexual assault and abuse for two decades. Additionally, Kelly pled not guilty in February to 10 counts of aggravated sexual abuse allegedly involving three girls and one woman over roughly 10 years starting in the late '90s.
R. Kelly has denied the allegations made in the six-part series.
In an earlier case, a Cook County jury in 2008 found Kelly not guilty of making child pornography. The obstruction charges would likely be on different grounds, at least, which suggests that the US Attorney has a different set of charges.