"The sum total of everything we have agreed upon has the same effect" as what Seehofer has demanded, Merkel said in an interview with ZDF television.
Applicants in these centers-which would be built on the border with Austria-could then be turned away and sent back to whatever European Union country they came from.
But Kurz warned "other countries, like Austria, will react by national measures" if Berlin confirms it will turn away asylum seekers arriving at the German border if they were registered elsewhere.
But the German news agency dpa reported that Seehofer told the meeting of CSU officials that he thinks the measures do not adequately accomplish his goals. At the same time she underlined the necessity of protecting Europe's outer borders more effectively as well as sealing partnerships with African countries to tackle illegal migration and lessen the incentives for economic migration. She also would not speculate on whether she might fire him or if the issue could lead to a government confidence vote in parliament.
Angela Merkel returned from Brussels with an agreement forged, or critics would say fudged, with her European counterparts about the handling of refugees and migrants.
Only once before has the cooperation been at risk - in 1976 when Bavarian leader Franz Josef Strauss thought the CSU would fare better in elections if it were free of the CDU. Seehofer is a member of the Christian Social Union, an ally of Merkel's party.
Despite those steps, both sister parties took a beating in September 2017 elections as millions of voters switched to the far-right AfD party, which is also running against the CSU in Bavarian elections in October, threatening to destroy its governing majority.
Among the proposals is a plan to send back to Austria asylum seekers arriving in Germany who can not be returned to their countries of entry into the European Union.
If Merkel holds firm and Seehofer does quit, the CSU could offer a replacement interior minister if it aims to remain tied to her party.
A real possibility is a break up of the 70-year alliance between the CSU and Merkel's CDU.
Bavaria's CSU Prime Minister, Markus Söder, said "we're ready for compromises" and "for us now there is no exit from the government".
Speaking about the meddling, Bolton told the Fox News Sunday programme: "I think it's something that we're concerned about. Bolton, without directly addressing the president's comment, said that was "not the position of the United States".
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