In a case that made waves earlier this month, German authorities acknowledged that the 22-year-old asylum seeker, who was not named, was deported to China by the German state of Bavaria due to an administrative error.
The Uighur's lawyer Leo Borgmann has said he has had “no sign of life” from his client since the expulsion and fears that he has been “detained” by Chinese authorities.
After an outcry by human rights groups and opposition politicians, the interior ministry said in a written response to a query by Greens MP Margarete Bause, that the practice had been halted.
“Until further notice, we will desist from repatriating Uigurs and their families,” the ministry said.
It cited “recent” guidance by Germany's Federal Office for Migration and Refugees (BAMF) and the foreign ministry on the situation in China in its decision not to send Uighurs back.
“The highly critical situation in terms of human rights, which are stressed in the BAMF report, has been known to German authorities for months,” Bause told AFP, citing a “danger to life and limb” for Uighurs in China.
“The fact that the Uighur was expelled by the Bavarian authorities in the dead of night is scandalous.”
Bause called on the German government to do “everything in its power” to secure the return of the deported man from China.
Many of the Uighur minority say they face cultural and religious repression in China.
Members of the Uighur diaspora say relatives have been arrested for seemingly innocuous acts such as sending Ramadan greetings to friends or downloading popular music.
Chinese authorities are also believed to have detained hundreds of thousands of Muslims in a secretive network of extra-judicial political re-education centres, where inmates are given language and ideological training and forced to participate in military-style drills.
The German foreign ministry recently updated its travel advisory for China's far-west Xinjiang region.
“In Xinjiang there have for months been rising numbers of arrests and passports revoked,” it said.
“Those affected are, in particular, people of Uighur origin.”
China has pointed to a series of attacks in Xinjiang by suspected Islamist radicals in recent years as justification for a draconian clampdown in a region with a long history of tensions with Beijing.