Horst Seehofer, of Merkel's conservative Bavarian sister party the CSU, also promised a broader "zero-tolerance" law and order drive under their new government to be launched Wednesday.
Most of those who came across the Balkans route passed through Seehofer's southern state of Bavaria, at times more than 10,000 a day, sparking a strong backlash in the region.
In an interview with newspaper Bild am Sonntag, Seehofer said that as the new head of an expanded ministry of interior and homeland affairs, he was working on a "masterplan for speedier asylum procedures and consistent deportations".
Repatriations and deportations must be "raised significantly", he said, vowing to especially "get tougher" on those who break German law or are deemed a security threat.
"We want to remain a country that is open to the world and liberal," Seehofer said. "But when it comes to protecting the citizens, we need a strong state. I will take care of that."
Germany's mass migrant influx brought more than a million people to Europe's biggest economy, about half of them from war-torn Syria, Iraq and Afghanistan.
It sparked a backlash and bolstered the rise of the anti-immigration Alternative for Germany (AfD) party, which entered parliament last September with almost 13 percent of the vote.
Merkel's fourth-term government, a coalition with the centre-left Social Democrats that is due to be sworn in this week, has vowed to keep the annual intake of new asylum seekers below 200,000.
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