A government official said Merz would not travel to New York as planned because "his presence is required in Berlin".
Merz had been expected to speak at the General Assembly on September 23.
There was no word on why his presence in Germany was required.
But speculation has mounted that Merz's job is in danger following a stinging defeat of his centre-right party by the far-right Alternative for Germany, or AfD, party in an election September 6 in the eastern region of Saxony-Anhalt.
That damaged the already unpopular chancellor's authority as he tries to push through reforms to Germany's sluggish economy.
Two more regional elections follow on Sunday: one in Mecklenburg-Western Pomerania, another largely rural eastern state, and the other in Berlin, the capital.
AfD is expected to make significant gains in both, though it has no realistic path to power in Berlin and faces a much stronger challenge from the current centre-left governor in Mecklenburg-Western Pomerania than it did from Merz's party in Saxony-Anhalt.
The prospects for Merz's Christian Democratic Union are bleaker, 16 months after the 70-year-old became Germany's leader.
It could lose the mayor's office in Berlin that it has held since 2023 and, if things go very badly, fail for the first time to win seats in a state legislature anywhere by falling below five per cent of the vote in Mecklenburg-Western Pomerania, a region where it was already weak.
Merz said last week that "giving up is not an option for me".
But the CDU's deputy local leader in Mecklenburg-Western Pomerania called for him to go, and speculation has mounted that he might soon be replaced - although no top-level allies have called publicly for his departure.
On Wednesday, his party's eight state governors gave Merz their public backing.
"People can trust that we will tackle their problems," they wrote in a joint statement, the German news agency DPA reported.
"As governors, we want to and will make our contribution together with the chancellor."
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