A ministry spokeswoman said the federal migration and refugee agency (BAMF) “will quickly take the necessary steps to bring back” the 20-year-old identified only as Nasibullah S.
The young man had been flown to Afghanistan along with 68 other failed asylum seekers in early July despite an ongoing legal appeal against his deportation.
Germany's hardline Interior Minister Horst Seehofer, who has repeatedly challenged Chancellor Angela Merkel's more liberal stance on migration issues, admitted that “apparently there were bureaucratic mistakes made at the BAMF” in its handling of the case.
The BAMF has said that it believed Nasibullah S. filed his appeal against being returned to Afghanistan too late under German law and thus ordered his deportation.
Seehofer, who has spearheaded a drive to rid Germany of rejected asylum seekers, came under fire last week with a quip about the deportation flight with 69 Afghans on board falling on his 69th birthday.
One of the other returnees, a 23-year-old man, committed suicide the day after Seehofer's press conference and outraged opposition politicians called for the minister's immediate resignation.
In a further controversial case, a German court last Friday ordered that a man who allegedly worked as a bodyguard for Osama bin Laden be returned only hours after his deportation to Tunisia, saying the expulsion was illegal as he risks torture there.
And last month, an Afghan man who was allowed back into Germany after he was illegally expelled from the country was officially granted asylum, at the end of a long odyssey through the courts.
Civilians continue to bear the brunt of the bloody conflict in Afghanistan that has been raging since 2001, making the issue of deportations from Germany and other European countries highly controversial.
In 2016, Berlin signed a deal with Kabul to repatriate Afghans who had failed to obtain asylum, and began expelling people in December of that year.
So far this year, 148 Afghans have been deported from Germany, official figures show.
Some of the deportees have spent most of their lives living outside of Afghanistan.
More Afghans are likely to be deported after Merkel's shaky three-party coalition agreed this month on a tougher migration policy that will reduce the number of asylum seekers in the country.