Churchill, an ethnic studies professor at the state-funded university, said in an interview that the allegations were a pretext to remove him because of his unpopular views.
"I'm not a martyr or a victim, but certainly a target," he said.
But three faculty committees had accused Churchill of falsification and other misconduct regarding some of his earlier writings, though the investigation only began after the controversy over his September 11 essay.
Hank Brown, the university president, said there had been little choice but to fire Churchill to protect the integrity of the university's research.
"The decision was really pretty basic," he said. "The individual [Churchill] did not express regret, did not apologise, did not indicate a willingness to refrain from this type of falsification in the future."
The allegations against Churchill included claiming the work of a Canadian environmental group as his own, misrepresenting the effects of federal laws on American Indians and fabricating evidence that the army deliberately spread smallpox to Mandan Indians in 1837.
His September 11 essay, Some People Push Back: On the Justice of Roosting Chickens, was not part of the investigation.
Controversy
That essay, along with a follow-up book, argued that the September 11, 2001, attack on the World Trade Centre was a response to a long history of US abuses.
He said that some of those killed in the attack were "a technocratic corps at the very heart of America's global financial empire", calling them "little Eichmanns", referring to Adolf Eichmann, the Nazi bureaucrat involved in the persecution of the Jews and the Holocaust.
Churchill explained that while Eichmann carried out policies planned by others, he was still responsible for his own actions.
Later, he conceded that the analogy was an "ill-designed rhetorical device", but continued to conclude that the attack was understandable, given US foreign policy in the Middle East.
The essay cause uproar and prompted some, including Bill Owens, then governor of Colorado, to call for Churchill to be sacked.
University officials said Churchill's writing was protected speech under the First Amendment, but launched an investigation into his research in other work.
David Lane, Churchill's lawyer, said that the decision was retribution for Churchill's September 11 remarks and that he would file suit on Wednesday.