The 23-year-old Afghan man was found dead in Kabul shortly after he was flown back. Afghanistan said he had lived in Germany for eight years, having arrived as a teenager.
He was one of 69 people flown by Germany to Afghanistan last week on interior minister Horst Seehofer's 69th birthday, an event which Seehofer had promoted at a news conference as evidence that he was increasing the pace of expulsions.
Seehofer, whose tough stance on immigration nearly brought down Angela Merkel's government last week, defended himself on Wednesday in Innsbruck, Austria at a migration summit with fellow hardline interior ministers from Austria and Italy.
He said local authorities in the city of Hamburg had put the man who killed himself on the deportation list
"The whole procedure is very regrettable," Seehofer said. "But you have to ask the Hamburg authorities why they suggested him." He refused to comment on his "birthday" remark, saying anything he said would be "misused".
Asked about calls for him to resign, he said: "I have nothing to say to that."
Seehofer is the leader of the CSU, a party which occupies the place of Merkel's conservative CDU in Bavaria, Germany's largest state. The two parties have been aligned almost without interruption since World War Two, but nearly fell out last week over Seehofer's tough line on immigration, potentially bringing down the government.
Gyde Jensen, a lawmaker for the pro-business Free Democrats and head of the parliamentary human rights committee, was one of many politicians who demanded Seehofer's dismissal.
"Anyone who celebrates 69 deportations for his 69th birthday is in the wrong job," she said in a statement.
