The CNN report claims that Clarke footnoted his sources in the thesis, titled "Making U.S. security and privacy rights compatible," but failed to use quotation marks in places where he had used passages verbatim, which breaks with school guidelines.
The Naval Postgraduate School in Monterey, California, where Clarke earned a master's degree in security studies in 2013, confirmed on Sunday to the Associated Press that the allegations published on CNN are being reviewed. The school removed his thesis from its online archive on Friday, a school spokesman told the AP.
Clarke responded to the allegations in an email to his hometown paper, the Milwaukee Journal Sentinel, by claiming that the story was partisan in nature.
"Only someone with a political agenda would say this is plagiarism," he wrote.
Clarke also referred to Kaczynski as a "hired gun" in a post in which he linked to a story published on a site called GotNews, which is run by conservative provocateur Charles "Chuck" Johnson.
Kaczynski on Sunday retweeted Clarke, and said that the sheriff had not addressed the issues raised in the story.
"Sheriff Clarke has yet to respond to the substance of our story," he wrote.
The Department of Homeland Security has not confirmed Clarke's appointment as assistant secretary.
Deaths in jail
Clarke's office has come under scrutiny over four deaths that have occurred in his jail since 2016, including an incident in which an inmate gave birth to a stillborn baby.
Among the most high profile incidents to take place in Clarke’s custody was the death of Terrill Thomas, a 38-year-old man who died of thirst in Milwaukee County Jail in April 2016.
Thomas was found dead in his jail cell nine days after he was arrested in connection with a shooting. The death was ruled a homicide, with dehydration the primary cause, according to the Milwaukee Journal Sentinel.
Clarke has not commented on the details surrounding Thomas' death, and issued a press release in September of 2016 citing an internal investigation of the case as the reason for his silence.
This month, a Milwaukee jury recommended criminal charges against seven Milwaukee County jail staffers in the death of Thomas, but ignored Clarke.
Clarke told Watchdog.org, a non-profit organization focused on transparency, that the narrative surrounding the deaths that have taken place in his jail was formed as a result of political prejudice.
“This has everything to do with politics and my support of Donald Trump,” the sheriff told the website. “These people are invested in bringing me down.”