Germany's migration row mirrors squalls seen across Europe since Merkel's decision in 2015 to open Germany's borders to more than a million migrants fleeing wars in the Middle East, transforming the demographic landscape nearly overnight.
But the interior minister was forced to cancel a planned presentation of his vision after Merkel disagreed with his proposal to turn some asylum seekers away at the borders, sparking last week's dramatic escalation of discord within the conservative bloc.
The disagreement has opened up a serious rift between Mrs Merkel's Christian Democrats and Mr Seehofer's Bavarian CSU party - two parties that have been closely aligned since the end of the World War Two.
Seehofer's "migration master plan", which Merkel last week refused to endorse, would see asylum seekers arriving at Germany's borders turned away if they have no identification papers, have already had an asylum claim rejected in Germany, or are already registered in another country in the EU - proposals that rights group say contravene European and worldwide agreements.
Merkel later on Monday met Italian Prime Minister Giuseppe Conte for talks in Berlin and said Berlin wanted to support Rome in its efforts to reduce the number of migrants arriving on its shores, possibly handling asylum requests for the European Union in non-European countries including Libya.
Instead, she wants to find a common European solution at the June 28-29 EU summit.
"Whoever knows Europe, realizes this is no easy task", Merkel told reporters in Berlin yesterday after a meeting of her Christian Democratic Union's executive.
Several high profile crimes by migrants have also fuelled public anger.
The CSU - which faces an election threat from the AfD in October state polls - has refused to budge and set Merkel an effective ultimatum of next Monday.
"I can not say that we have a grip on the issue", he told a press conference after huddling with top brass of his CSU party.
Former chief strategist Stephen Bannon: "We ran on a policy - very simply - stop mass illegal immigration and limit legal immigration, get our sovereignty back to help our workers, and so he went to a zero tolerance policy".
German Interior Minister and leader of the Christian Social Union (CSU) Party Horst Seehofer gestures after giving a press conference after the party meeting at the CSU headquarters in Munich on June 18 2018.
German news agency dpa reports that Interior Minister Horst Seehofer has told his party he wants to proceed step-by-step in his plan to turn back some migrants at the country's borders - hinting at a compromise in a dispute with Chancellor Angela Merkel.
It comes after Merkel's coalition partners threatened to start turning some migrants away at the German border.
"By granting Merkel her two weeks, the CSU is ostensibly making effective bilateral deals their condition for staying in the grand coalition", said Mujtaba Rahman, managing director at Eurasia Group.
Merkel was reportedly planning to contact all her European Union counterparts over the next few days in the hope of striking a series of bilateral deals, ahead of a crucial European Union summit at the end of June at which she hopes to come to an agreement to end the impasse.
If Seehofer, who has always been critical of the chancellor, decides to defy her, it could spell an end to the 70-year alliance between his Bavarian conservatives and those whom she represents in the remainder of the country.
There is even talk that the 70-year-old conservative parliamentary alliance between the CDU and CSU could collapse.