The 23-year-old was among 69 Afghans deported last week as part of a tougher line on migration.
His death – at a hotel in Afghanistan’s capital Kabul – has prompted calls for German Interior Minister Horst Seehofer, who pressed for stricter immigration rules, to resign.
Mr Seehofer launched his “Migration Masterplan” earlier this week, with the promise that it would toughen border and immigration controls.
It clashed with the open-door policy Ms Merkel has pursued since the height of the 2015 refugee crisis.
Mr Seehofer claimed credit for an increase in the pace of deportations of rejected asylum-seekers earlier this week and appeared to joke about the matter.
“Just on my 69th birthday – and I didn’t request it – 69 people were sent back to Afghanistan,” he said. ”That’s way above earlier levels.”
A German interior ministry official announced the death of the 23-year-old to journalists at a news conference, saying: “We received confirmation from the Afghan authorities this morning that one of passengers on the repatriation flight was found dead in accommodation in Kabul. According to the Afghan authorities, it was a suicide.”
Mr Seehofer did not immediately comment on the matter. He has repeatedly clashed with Ms Merkel and their Social Democrat (SPD) coalition partners in his drive to raise his Christian Social Union’s party profile and head off a far-right challenge in a regional election.
But Gyde Jensen, a lawmaker for the liberal Free Democrats and head of the parliamentary human rights committee demanded Mr Seehofer’s be fired.
“Anyone who celebrates 69 deportations for his 69th birthday is in the wrong job,” she said in a statement. “How many more derailments does the coalition need to dismiss the interior minister... The limit has been reached.”
Some 17 years after the Taliban were ousted by a US-led campaign following the September 11 attacks on the United States, hundreds of civilians have been killed in attacks this year in the capital Kabul as well as other cities.
Despite an intensive US bombing campaign, aimed at forcing the Taliban to accept peace talks, the insurgents control wide stretches of the country.
Last year, after a bombing in the Afghan capital of Kabul killed at least 80 people, Ms Merkel said Germany would deport to Afghanistan only criminals and people it considers a threat.
But Germany has recently abandoned those restrictions based on a new assessment of the security situation in Afghanistan, the interior ministry said.
The forced removals have triggered protests at airports, with demonstrators holding signs with messages such as:”Don’t send people back to die.”