The London-based rights group called on China to free the 56-year-old activist Hada, his wife Xinna and son Uiles, who were detained around the time of Hada's scheduled prison release on Dec. 10 after a 15-year term.
"Amnesty International fears they may be subjected to enforced disappearance," the group said in a statement.
While separatism among Mongolians living in Chinese-controlled Inner Mongolia is not well known, it's a sensitive issue for China's government, which fears the spread of the violent ethnic unrest that has hit Tibet and Xinjiang in recent years.
Hada, who like many Mongolians uses just one name, campaigned for Inner Mongolia's independence from China before being jailed in 1996 on charges of separatism and spying.
Amnesty International said Hada's sister-in-law, Naraa, was told on Dec. 14 by an official from the Inner Mongolia Autonomous Region Public Security Bureau that Hada and his family were "enjoying a family reunion" in a hotel and that they needed time to "plan their next step."
The official did not go into specifics, the group said.
Calls to the region's public security bureau rang unanswered Monday while the mobile phones of Xinna, Uiles and Naraa were switched off.