Merkel, who ran unopposed, won 89.5 per cent of delegates' votes at a congress of her Christian Democratic Union in the western city of Essen for a new two-year term.
That was short of the 96.7 percent she won in 2014, but still a solid mandate as she prepares to seek a fourth term as chancellor in next year's German election.
The vote came after a speech in which she struck a decidedly conservative note, telling members that she wants to stem the influx of migrants and restrict use of face-covering veils such as the burqa and niqab.
Germany saw about 890,000 asylum-seekers arrive last year. Many came after Merkel decided in September 2015 to let in migrants who were stuck in Hungary. The numbers have since declined sharply, but Merkel's "we will cope" approach to the migrant crisis has provoked discord within the CDU, which has seen a string of poor state election results this year.
"A situation like the one in the late summer of 2015 cannot, should not and must not be repeated," Merkel told delegates.
Merkel was also a driving force behind an agreement between the European Union and Turkey in March to stem the flow of migrants.
Polls show a solid lead for the conservatives, although their support is still short of the 41.5 percent they won in Germany's 2013 election. They face new competition from the upstart nationalist Alternative for Germany party, which has thrived by attacking Merkel's migrant policies.
Merkel told delegates that "parallel societies" won't be tolerated and advocated banning the wearing of full-face veils used by some Muslim women where that's possible. But she also hit out at anti-migrant and anti-government protesters who chant "We are the people!" or post hate messages on social media.
"Who the people are ... Is something that we will all determine, not just a few, however loud they may be," she declared.
The EU's longest-serving head of government has often said her aim is for Europe to emerge stronger from crises such as the debt troubles that afflicted the common euro currency. "We must, in this situation ... First do everything so that Europe doesn't emerge even weaker from the crises than when it went in," she said.
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