According to a new filing by lawyer Beau Brindley, the 58-year-old singer - who is serving 30 years in a North Carolina prison for sex trafficking and racketeering - was placed in isolation on June 10 with his anxiety medication.
After being given more medication by prison staff, he lost consciousness three days later and was taken to Duke University Hospital on June 13.
After two days under observation, he was taken back to his cell.
The lawyer claims that officers intentionally "gave him an amount of medicine that could have killed him".
He said in the documents: "This was no mistake. It was a dose that jeopardised his life and nearly ended it."
Brindley subsequently filed an emergency motion for Kelly's early release from prison.
It is a third attempt to get his client out from behind bars.
Kelly is already seeking clemency from US President Donald Trump as he fears for his life in federal prison.
The rapper's lawyer filed an emergency motion alleging three officials from the Bureau of Prisons (BOP) plotted to murder him while incarcerated.
Brindley told People: "We believe that President Trump is the only person with the courage to help us."
Kelly's legal team hopes a pardon or commutation might be granted by Trump.
Brindley added: "Immediately after our motion became public, Robert was thrown into solitary confinement.
"He cannot make phone calls to his family. He has no access to commissary. He has spiders crawling over him while he tries to sleep."
Kelly is reportedly afraid to eat prison food over fears it might be poisoned, according to his lawyer.
The emergency motion included a declaration from inmate Mikeal Glenn Stine, who alleged he was asked to kill Kelly by three high-ranking BOP officials.
Stine, who claimed membership in the Aryan Brotherhood and said he was once a commissioner with the group, stated prison officials arranged his transfer to the Federal Correctional Institution Butner in North Carolina - here Kelly is also held - and placed him in Kelly's unit.
In return for carrying out or arranging the murder, Stine alleged he was promised an escape from custody and the chance to live as a "free man".
Stine also claimed he has terminal cancer and later told Kelly about the plot, stating he no longer intended to go through with it.
Last month, Trump said he would consider pardoning Sean "Diddy" Combs, who faces similar federal charges.
"If I think someone was mistreated it wouldn't matter whether they like me or don't," Trump said.
Brindley added about Kelly's situation: "He is not safe in federal custody. And to keep him in prison while he is under threat like this is cruel and unusual punishment."
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