The interior ministry said a plane carrying the men took off Friday morning bound for Afghanistan, adding that all the deportees were under expulsion orders and were convicted by the criminal justice system.
The government of Europe's top economy was forging ahead with a "policy change", said Interior Minister Alexander Dobrindt, who was hosting several European counterparts for a migration meeting.
"Deportations to Afghanistan must continue to be carried out safely in the future. There is no right of residence for serious criminals in our country."
Berlin has had only indirect contact with the Taliban authorities through third parties with Friday's operation executed with the help of Qatar, said the German interior ministry.
Germany had stopped deportations to Afghanistan and closed its embassy in Kabul following the Taliban's return to power in 2021.
But expulsions resumed last year for the first time since the Taliban came to power, when the previous government of Social Democrat chancellor Olaf Scholz expelled a group of 28 Afghans convicted of crimes.
Rights concerns
Human rights group Amnesty International strongly criticised the renewed deportations to Afghanistan saying the situation in the country was "catastrophic".
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"Extrajudicial executions, enforced disappearances, and torture are commonplace," the group said in a statement.
At the beginning of the month, the International Criminal Court issued arrest warrants for two senior Taliban leaders in Afghanistan, accusing them of crimes against humanity over the persecution of women and girls.
Merz told a press conference on Friday that Germany wants to be an "attractive country for immigration", to attract the best talent and fill gaping labour shortages,
The previous government's policies had however left local administrations with too large a burden to carry, Merz said.
His government had "initiated corrections" to put migration policy on the right course, he said, including tightening border controls and limiting family reunifications rights for some refugees.
Merz said that policing Germany's borders with its neighbours was only a "temporary" solution and a durable solution was needed at the European level.
Migration summit
Dobrindt was meeting his French, Polish, Austrian, Danish and Czech counterparts, as well as European Commissioner for Home Affairs Magnus Brunner, in southern Germany on Friday.
The objective of the meeting is to "strengthen European migration policy," Dobrindt told the Augsburger Allgemeine daily.
A debate over resuming expulsions has flared as migration has risen up the political agenda in tandem with the rise of the far-right Alternative for Germany (AfD) party.
The AfD scored a historic election result of over 20 percent in February -- its highest score at a national level -- leaving the party nipping on the heels of Merz's conservative CDU/CSU bloc.
The controversy over immigration was fuelled by a series of deady attacks last year where the suspects were asylum seekers -- including several from Afghanistan.Â
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Germany's new government, a coalition between the CDU/CSU and the centre-left Social Democrats (SPD), has promised to expel more foreign criminals alongside a crackdown on irregular migration.
As well as carrying out deportations to Afghanistan, Dobrindt has said he was in contact with authorities to enable deportations to Syria, which have been suspended since 2012.
Longtime Syrian ruler Bashar al-Assad was toppled in December. The country is now under the control of Islamist leaders, some of whom were once linked with the Al-Qaeda jihadist network.
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