According to three unnamed sources who spoke to the paper, the fallen financier was physically assaulted by another inmate last December.
According to one of the sources, who is an inmate familiar with the matter, Madoff was treated for a broken nose, fractured ribs and cuts to his head and face.
The 71-year-old Madoff is currently serving a 150-year sentence in a North Carolina federal prison after admitting his multi-decade pyramid scheme cost thousands of investors billions of dollars.
The Wall Street Journal said details of Madoff's injuries could not be independently confirmed. Officials are denying the incident, claiming Madoff was suffering from dizziness and hypertension.
On Wednesday, two former employees accused of helping the fraudulent Wall Street financier program an old computer to generate false records were indicted.
The indictment accuses computer programmers Jerome O'Hara and George Perez of conspiracy, falsifying records of a broker dealer and falsifying records of an investment adviser.
O'Hara and Perez each remain free on $1 million bail. Defense lawyers say the men will plead not guilty.
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