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.
Seehofer was long the harshest critic within Merkel's conservative bloc of her decision to open Germany's borders to a mass influx of refugees and migrants since 2015.
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.
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.
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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