Swartz was accused of illegally downloading about 5 million academic articles from a paid database, called JSTOR, using computers at the Massachusetts Institute of Technology where he was a student. Swartz's family requested the list be made public due to the intense interest the case has generated.
Swartz's supporters said prosecutors and school officials were overzealous and sought to make him an example for other activists -- leading the 26-year-old to take his own life in January.
U.S. District Judge Nathaniel Gorton said the risk of reprisals for those on the list outweighed the public interest in the case, The Wall Street Journal reported Monday.
"Although the public has expressed a strong interest in the investigation and prosecution of Mr. Swartz, that fact does not bestow upon his estate the right to disclose criminal discovery materials produced to his counsel solely for the purpose of preparing for trial," Gorton wrote. "This is particularly true where disclosure may subject third parties to threats and harassment."
An attorney representing the Swartz family couldn't be reached to comment.
A House committee is investigating the Justice Department's handling of the case, an inquiry that coincides with MIT's own internal investigation into Swartz's alleged crimes and how they were handled.
Since Swartz's January death, MIT has been hacked several times and been subject to bomb threats. Some specific individuals with MIT and JSTOR have faced personal threats, as well, the Journal said.