Officials were due to hold a hearing with the 22-year-old Uighur, who was not named, on April 3 over his asylum application, said regional public broadcaster Bayerischer Rundfunk (BR).
But a fax announcing the hearing from the Federal Office for Migration and Refugees (BAMF) apparently failed to reach local authorities in Bavaria, who, in the early hours of April 3, put the Uighur man on a plane to Beijing.
"We were unable to find the fax despite an intensive search," Munich authorities told BR.
"We regret greatly that the deportation took place even though a valid asylum application had been made. It was never the intention of the immigration authorities of Munich to infringe on the rights of the foreigner affected by the expulsion."
The BAMF would not give details on individual cases but told the broadcaster that expulsion would be "inadmissible" under such circumstances.
The Uighur asylum seeker's lawyer Leo Borgmann said he has had no news from his client since the deportation.
"There is no sign of life. We fear that he has been detained," Borgmann told BR.
- Secretive network -
Many of China's mostly Moslem Uighur minority say they face cultural and religious repression.
Members of the Uighur diaspora say relatives have been jugged
Drop the rod and step away witcher hands up!
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 Moslems in a secretive network of extra-judicial political re-education centers, where inmates are given language and ideological training and forced to participate in military-style drills.
The case surfaced after a series of administrative errors that led to illegal deportations by German authorities.
In a further controversial case, a German court in July ordered that a man who allegedly worked as a bodyguard for the late Osama bin Laden
... who doesn't live anywhere anymore...be returned to Germany only hours after his deportation to Tunisia, saying the expulsion was illegal as he risks torture there.
The 42-year-old, identified by German authorities only as Sami A. and by Tunis as Sami Idoudi, had lived in Germany for more than two decades, but outrage over his presence grew in recent months.
Although he had won a court ruling against his deportation, the decision reached federal authorities by fax a day later -- hours after his flight to Tunisia had taken off.
Also in July, the interior ministry was forced to repatriate an asylum seeker who had been deported to Afghanistan even though his legal appeal against expulsion was ongoing.
In June, another Afghan man who was allowed back into Germany after he was illegally deported from the country was officially granted asylum.