Thanking the NYU for its support, the 41-year-old lawyer-activist in a statement said the university which is opening campus in Shanghai is bowing to pressure from the China's ruling Communist Party (CPC).
"As early as last August and September, the Chinese Communists had already begun to apply great, unrelenting pressure on New York University, so much so that after we had been in the US just three to four months, NYU was already starting to discuss our departure with us," the South China Morning Post daily quoted Chen as saying in the statement.
Chen, who crated a sensation last year by sneaking into the US Embassy just coinciding with the visit of the then US Secretary of State Hillary Clinton, alleged the CPC's influence in US academia was "far greater than what people imagine".
He was allowed to leave for US by Chinese leadership under pressure from the US which promised him facilities for education.
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"Academic independence and academic freedom in the United States are being greatly threatened by a totalitarian regime," he said.
"(But) I will never bow my head to evil or to lies. I will always do everything I can for my compatriots back in China who still are not free," he said in the statement.
Chen has become a rallying point for Chinese dissidents.
After his visit to the US, he had travelled to Germany and Britain to give speeches and collect awards. He is due to travel to Taiwan later this month.
NYU spokesman John Beckman said the university was "very discouraged" by Chen's statement, which he said contained speculations that were "both false and contradicted by the well-established facts".
"Chen's fellowship at NYU and its conclusion have had nothing to do with the Chinese government. All fellowships come to an end," he said, quoted by the Post.
He said NYU had been providing Chen's family with housing, food, health care, insurance and translation services as well as tutorials in law and English-language lessons.
"NYU believes it has been generous in supporting this family, and we are puzzled and saddened to see these false claims directed at us," he said.