He said he still believed a solution could be found on the migration issue.
A new poll by the INSA institute showed the dispute was weakening support for the CSU in Bavaria, with its polls down one percentage point to 41 percent since April, and the AfD poised to become the second largest party in the state with 14 percent.
Yet in spite of the threat of being sacked from cabinet and triggering the collapse of the German federal government, the CSU leader has warned that he will press ahead unilaterally with his "migration master plan" unless Merkel secures a binding and comprehensive agreement from other European Union member states at the Brussels summit.
The Forsa poll, published after Ms Merkel and other European Union leaders failed to come up with a bloc-wide policy on immigration at a conference in Brussels, showed the issue was still top of the agenda in Bavaria.
The poll showed that the CSU has lost support in the region, with 40 percent of Bavarian respondents saying they would vote for the party - a drop of 7.7 percentage points compared to the 2013 regional election results.
CDU general secretary Annegret Kramp-Karrenbauer said the CDU had agreed it was necessary to control and reduce migration to avoid a repeat of the 2015 situation, when hundreds of thousands of migrants arrived in Germany, but declined to speculate on what would happen if the CSU rejected Ms Merkel's proposals at a meeting next Sunday.
The survey also revealed that Merkel is more popular among Bavarians than Seehofer or state premier Markus Söder, also of the CSU: While 43 percent of Bavarian respondents said they were happy with Merkel's work, 37 percent said the same about Seehofer and 38 percent approved of Söder's work.
If Seehofer goes ahead with his plans, many members of Merkel's CDU say she would be forced to fire him.
Amid signs of nervousness from some in the CSU over their collision course with Merkel's Christian Democrats (CDU), Merkel sent a conciliatory message to the CSU, describing its 70-year-old alliance with her Christian Democrats (CDU) as a "bond of fate".
Chancellor Merkel has strongly opposed Seehofer's plan and said such a unilateral move would have "a domino effect", prompting other European Union member states to push back refugees and further increase the burden of member states like Italy and Greece.
Nearly three years after German Chancellor Angela Merkel's fateful welcome to a million migrants, her boldest move has come back to haunt her, with opponents at home and overseas smelling blood.
Even then, Germany is still home to the majority of Europe's refugees.