Mr. Kelly is scheduled to be brought before a federal judge in Chicago on Friday to be arraigned on the new indictment. Officials said he would ultimately be brought to New York City to face charges, though it was unclear when. He was not expected to appear in court in Brooklyn on Friday.

The federal charges, which officials said would be unsealed on Friday, deepen the legal morass for Mr. Kelly, who has been dogged by allegations of sexual misconduct for decades but was acquitted on state child pornography charges in 2008.

Mr. Kelly, 52, whose real name is Robert S. Kelly, already faces more than a dozen state felony charges related to sexual abuse accusations in Chicago involving four women, three of whom were underage at the time, prosecutors said.

He was charged with 10 state counts in February, with more state charges filed against him in May. He has pleaded not guilty to those charges.

Mr. Kelly was arrested while walking his dog on Thursday night by New York detectives and federal agents from Homeland Security Investigations, who built the case with the New York Police Department, officials said.

Mr. Kelly’s lawyer, Steve Greenberg, said in a statement that Mr. Kelly was “aware of the investigations and the charges were not a surprise.”

Mr. Greenberg also said that most of the charges appeared to stem from old allegations, some of which were made in the previous indictment.