"If I'm not successful [in getting an answer from Berlin] then we will have to consider what options for action we have," Seehofer told the Passauer Neue Presse – implicitly reiterating his threat to bring in undefined "emergency defence" measures if the federal government doesn't help.
Seehofer added that Merkel's top priority ought to be limiting what he said were uncontrolled flows of people from Austria into Germany across the Bavarian border.
"It's the Chancellor's job to speak with Austria," he said, adding that the two national governments had decided to introduce the much criticized 'open-borders' policy together.
Austria's failure to warn Bavaria of large groups of refugees arriving at or being brought to the border was straining relations, Seehofer said.
"This behaviour by Austria burdens our neighbourly relationship. You can't and mustn't treat one another like this," he said.
The Bavarian premier can count on the support of a large proportion of his Christian Social Union (CSU), the Bavarian conservative party that is a historical ally of Merkel's Christian Democratic Union (CDU).
MPs from the Free State have been among some of the loudest voices criticizing the Chancellor's politics in recent weeks, stirring dissatisfaction among her own ranks.
"If our asylum policy isn't corrected," Seehofer said, then "the existence of the CDU and CSU" is threatened.
Merkel has made some steps towards placating the Bavarian premier, including a package of toughened asylum laws passed recently and an admission on Monday that her policy had been "anything but perfect".