The agency's representative in Kazakhstan, Cesar Dubon, said the UNHCR fears the man -- whose name he gave as Arkin Yarmamat Sabirov -- might have been deported.
The UNHCR voiced similar concerns on November 17, but Kazakh authorities apparently failed to address them.
Sabirov was detained in Almaty in June. The UNHCR says he disappeared immediately after an Almaty district court dismissed all criminal charges brought against him and ordered his conditional release.
Under international laws, asylum seekers cannot be deported.
China's Muslim Uyghur minority has long faced government persecution over its campaign for greater political and cultural rights.