The group said it spoke with Abuduwaili Abudureheman on Tuesday and was told he "did not travel to Hong Kong, contrary to previous information received".
Amnesty issued a news release Friday saying Abuduwaili had taken a flight to Hong Kong on May 10 and had not been heard from since.
It also said he had sent a text message saying he was "questioned by Chinese police".
The Hong Kong government condemned Amnesty's allegation as "groundless and unfounded" and said it "slandered the human rights situation" in the city.
Amnesty said in a statement on Tuesday: "We are pleased that Abuduwaili Abudureheman is accounted for."
A dean at Seoul's Kookmin University, where Abuduwaili studied, said he was "safe in Korea", according to South Korea's Yonhap news agency.
AFP has not been able to locate or contact Abuduwaili independently.
Amnesty said it would continue to monitor the human rights situation for Uyghurs, a Muslim minority in China that has been subject to large-scale detention by Beijing.
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