Kelly, 53, is in jail at the Metropolitan Correctional Facility in Chicago and faces charges in Illinois, Minnesota and New York stemming from alleged sexual abuses of underage girls.
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Last month, the singer's attorneys filed a motion calling to be granted his release because of COVID-19.
In her ruling Tuesday morning, Eastern District of New York Judge Ann Donnelly ruled that Kelly, "has not established compelling reasons warranting his release. At present, there are no confirmed cases of COVID-19 at the MCC in Chicago."
Kelly was arrested in July on sex charges. He denies abusing anyone.
The federal charges in Chicago accuse Kelly of filming himself having sex with underage girls and of paying off potential witnesses in his 2008 trial - at which he was acquitted - to get them to change their stories.
In December, he pleaded not guilty via a video feed to added charges in New York that he schemed to pay for a fake ID for an unnamed female a day before he married R&B singer Aaliyah, then 15, in a secret ceremony in 1994.
Previous coverage:
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R. Kelly cites coronavirus risk in request for release from Chicago jail
Reworked charges in Chicago cite another R. Kelly accuser in sex abuse case
R. Kelly's girlfriend charged after Trump Tower fight on singer's birthday
'Surviving R. Kelly Part II: The Reckoning' premieres on Lifetime
Federal records reveal wide scope of R. Kelly racketeering investigation
R. Kelly hit with new bribery charges in NYC, prosecutors say
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Judge denies bid to raise R. Kelly's bond in state case
R. Kelly trial date set on federal sex crimes charges filed in Chicago
R. Kelly facing new underage prostitution charges in Minnesota, prosecutors say
R. Kelly crisis manager stepping down
R. Kelly held without bond following Tuesday's arraignment on federal sex crime charges
The Associated Press contributed to this report.