The university, a private institution in Manhattan, said earlier this month that it would soon part ways with the blind activist, whose dramatic escape from house arrest to the US embassy in Beijing last year provoked a diplomatic crisis.
Chen, who arrived in the United States last May, claimed that Beijing applied "unrelenting" pressure on the university to end his programme.
NYU has adamantly denied the charge and a professor instrumental in bringing him to the law school, Jerome Cohen, has also denied political pressure.
"No one here from the government or the (ruling Communist Party) has ever spoken to me about him and his tenure at New York University in New York," NYU Shanghai Vice Chancellor Jeffrey Lehman said.
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"The communications were always between him and NYU in New York," he said in response to a question at a conference in Shanghai.
"NYU Shanghai was never involved so there was no role in the end of his fellowship," he said, adding that the university never planned to enroll Chen beyond a year.
The programme -- a joint venture with NYU's local partner, East China Normal University -- is set to welcome its first batch of students in the fall of 2013.
China has granted NYU Shanghai independent legal status to operate, and Lehman said the campus would preserve academic freedom despite operating in China.
"NYU operates as a liberal education institution that requires academic freedom in order to be effective," Lehman said.
"From the beginning, there was complete commitment on the part of our Shanghai and our Chinese colleagues to respect the value of academic freedom within our university," he said.