The report that CNN carried over the weekend cites close to 50 instances in Clarke's 2013 thesis where it seems he failed to put quotation marks around statements he took nearly verbatim from other sources.
Clarke appeared to have lifted lines from such diverse sources as the 9/11 Commission Report, a 2013 Washington Post article, and George W. Bush's book Decision Points.
According to CNN's KFile, which first reported the news late Saturday, there are at least 47 instances in Clarke's thesis on USA security where he failed to properly attribute a source that he directly quoted.
Clarke wrote in an email to The Milwaukee Journal Sentinel (http://bit.ly/2q5VT7h ) that "only someone with a political agenda would say this is plagiarism".
Clarke responded over the weekend by calling CNN reporter Andrew Kaczynski a "hack", and a "sleaze bag" in a series of tweets.
The school removed Clarke's thesis from its website shortly after CNN's story was published. A message on the school's online archive directed viewers to its policies page, which listed several reasons for taking an item down, including not meeting "the school's guidelines for plagiarism, research methodology or integrity of research".
The CNN report showed Clarke did not attribute text directly taken from a 2002 ACLU report about "The Government's Demand for New and Unnecessary Powers After September 11", a 2007 ACLU report on "fusion centers", a 2003 ACLU report critical of the FBI's records-collection practices, and a 2011 ACLU report on the need to maintain secrecy laws.
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WannaCry, developed in part with hacking techniques that were either stolen or leaked from the U.S. The United States accused it of being behind a cyber attack on Sony Pictures in 2014.
In the CNN report, Clarke is accused of allegedly neglecting the basic requisites of proper attribution.
Clarke has a loyal national, right-wing following but has been widely criticized locally for his inflammatory rhetoric and for spending so much time on the road as a Trump surrogate and while giving talks to conservative groups.
The Department of Homeland Security has not confirmed his appointment.
Clarke now oversees the Milwaukee County Jail, where one newborn baby and three inmates have died since April 2016.
Kaczynski on Sunday retweeted Clarke, and said that the sheriff had not addressed the issues raised in the story.
Critics have faulted Clarke for his management of a Milwaukee County jail where a mentally ill man died in 2016 of dehydration after seven days without water.
Prospective members of Trump's administration have previously faced allegations of plagiarism.