Merkel's welcome to refugees infuriated Seehofer and his CSU, the sister party of her Christian Democrats in the southern state of Bavaria, which became the main entry point for most migrants.
Merkel spokesman Steffen Seibert, who was at a government news conference at the time of Friday's tweet, said there were signs that the tweet actually came from a writer at the satirical magazine Titanic.
Soeder says his party, which is fearful of losing voters to the far-right Alternative for Germany in the Bavarian election on October 14, wants to "put the needs of our population center-stage". New right-wing leaders in neighboring Austria and Italy are pushing anti-immigration agendas, populist parties have gained ground across the European Union, and Merkel can't even rely on her conservatives to back her at home. The immigration issue is highly emotive, and the CSU's leaders believe the party needs to take a firm stance, which has the potential to cause a damaging rift with Merkel's CDU that threatens the future of the fragile coalition.
Its chairwoman Andrea Nahles said: "We won't allow the panic of the CSU's regional government to hold Germany and Europe hostage", she told reporters.
The dispute between Seehofer and Merkel lies in the fact that the head of the Ministry of interior requires permission for border lands such as Bavaria, to refuse asylum seekers, if they have registered in another European Union member state or if in Germany they have been refused asylum, writes Deutsche Welle.
Such a challenge could force her to fire Seehofer, or lead her Christian Democrats (CDU) to split up the parliamentary bloc in which they have cooperated with the CSU since 1949.
The CDU executive committee is solidly behind the chancellor -at least that is what Schleswig-Holstein State Premier Daniel Günther told the daily Neue Osnabrücker Zeitung.
For a while, it looked like the CSU was more likely to back down: German news agency DPA reported this week that the Bavarian party offered two compromises at a crisis meeting on Wednesday night - both involved asylum-seekers being turned away at the border - with the decision being reversed following at a vital European Union summit in a couple of weeks. "Asylum tourism must end".
German Chancellor Angela Merkel said on Friday that she wanted the European Stability Mechanism (ESM), the euro zone's rescue fund, to be transformed into a long-term instrument.
SPD Finance Minister Olaf Scholz added: "The task of governing our country is not an episode of Game of Thrones, but a very serious matter". "All those involved should never forget this".
Amidst the surprise announcement by the European Central Bank to detail its QE exit and alter its rate guidance, a report had surfaced that the German coalition that took 6 months to form could be on the brink of collapse with Bavarian sister party CSU threatening to break away due to different opinions over immigration policy.