The R&B star was arrested last week in Chicago and hit with 18 charges in two cities, a 13-count indictment in Chicago and a five-count indictment New York. Kelly has not yet faced a judge on the New York charges.
Assistant U.S. Attorney Angel Krull said Kelly is a flight risk who could tamper with witnesses.
"The risk for obstruction is real and ongoing,” Krull told U.S. District Court Judge Harry Leinenweber, arguing that “no release conditions can mitigate these dangers.”
Leinenweber said charges against Kelly are so serious, they require a presumption of detention.
After the hearing, defense lawyer Steven Greenberg insisted his client is not a flight risk, saying he's never missed a court date and doesn't even hold a passport.
"Obviously we’re disappointed the judge wouldn’t let him out today," Greenberg told reporters. "We thought we'd get him out but the judge saw it otherwise and we respect his ruling."
The singer is being kept apart from the rest of the jail population.
“He’s in 24-a-day solitary confinement essentially, it’s the hole," Greenberg said. "Because that's the safest place for them to house him, it’s not his fault, no TV, no anything, no contact with other people. It’s largely inhumane. "
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Kelly, already facing state sexual abuse charges in Illinois, allegedly took underage girls across state lines for sex, according to the federal indictments unsealed in New York and Chicago on Friday.
Two women who have said they are living with Kelly attended his arraignment Tuesday and sat in the front row. Azriel Clary and Joycelyn Savage have defended Kelly in the past from accusations that they have been brainwashed.
Savage and Clary sat in the front row, along with some of Kelly’s friends and family. They left the courthouse arm-in-arm and declined to answer questions from reporters.
“These young women have been traumatized and brainwashed for years. It is going to take them a while to realize how they have been victimized and what the truth really is," lawyer Michael Avenatti, who is representing Clary's parents, said.
The women appeared together on CBS in March and both said they're in a relationship with the singer. "We live with him, and we're in a relationship with him, we just said it," Clary said.
Kelly said in the fiery interview with Gayle King that "it's almost — it's like they're my girlfriends."
The 52-year-old R&B star, whose real name is Robert Kelly, and two of his employees are accused of recruiting women and girls to engage in illegal sexual activity with the performer and paying victims and witnesses to cover up his crimes.
An indictment unsealed Friday in the Eastern District of New York includes five criminal counts, including for racketeering, transporting underage girls for sex, and sexual exploitation of a child. The accusations go back as far as the late 1990s.
Once Kelly had convinced victims to be with him, they "were not permitted to leave their room without receiving permission from Kelly, including to eat or go to the bathroom," according to court papers.
Victims were also told to keep their heads down, to avoid eye contact with other men among other rules according to the New York indictment, which involves five unidentified victims.
Two of those victims in the New York case were 16 and another one was under 18, authorities said.
The illicit acts happened in New York, Illinois, Connecticut and California, according to federal prosecutors in New York.
"Kelly and the other members of the enterprise traveled throughout the United States and abroad to perform at concert venues, to promote the R. Kelly brand and to recruit women and girls to engage in illegal sexual activity," the New York indictment says.
It also alleges he engaged in "sexual activity with girls under 18 years old, engaging in and facilitating sexual activity without disclosing a sexually transmitted disease Kelly had contracted and producing child pornography."
In Chicago, he was hit with the 13 federal charges, including for sexual exploitation of children and possession of child pornography.
Authorities in Chicago accused Kelly of engaging in sex acts with five minors whom he met between 1996 and 1999, according to an unsealed indictment.
Kelly gave $30,000 to the father of one of the victims and transferred title of a GMC Yukon Denali to that child, according to the Chicago indictment.
Puskar reported from Chicago and Li reported from New York.
David K. Li
David K. Li is a breaking news reporter for NBC News.