Kelly is currently serving a 30-year prison sentence in a facility in North Carolina. He was found guilty of a variety of crimes, including federal racketeering and sex trafficking of minors.
His lawyers claimed in a series of filings on Monday and Tuesday that Kelly was in solitary confinement when prison staff instructed him to take an "excessive amount of medication" on June 12.
The 58-year-old was "lost" and "dizzy" the next morning, the file claims.
"Mr. Kelly tried to get up but fell to the ground. He crawled to the cell door and lost consciousness," his lawyers said.
Court documents say Kelly was taken by ambulance to Duke University Hospital and that he was under treatment for two days.
"For reasons of privacy, security, and protection, we do not discuss the conditions of detention for any incarcerated individual, including medical and health matters. In addition, the Bureau of Prisons does not comment on pending lawsuits or matters that are the subject of legal proceedings," the office said in a statement.
Kelly's lawyers had previously filed an emergency motion for release to house arrest, saying the once-famous artist was the target of a murder plot orchestrated by prison officials.
Opposing the request, government lawyers called the allegations "strange" and "theatrical."
The request "makes a mockery of the harm suffered by Kelly's victims," Chicago federal attorneys said, adding that it was not filed in the proper court with jurisdiction to hear the charges.
Kelly was convicted in 2021 in New York federal court of using an enterprise to systematically recruit and traffic teenagers and women for sex.
The singer known for hits including "I Believe I Can Fly" was convicted a year later in federal court in Chicago in a separate trial, in which a jury found him guilty of producing child pornography and luring a minor.
He is currently serving a prison sentence in New York and will serve almost all of his sentence in Chicago concurrently.