If the federal government does not take the initiative itself to control the number of people coming into the country, the Bavarian government will force it to through the Constitutional Court, the Bavarian government announced on Friday after an emergency meeting of the state cabinet.
Bavarian Minister President Horst Seehofer, of the Christian Social Union (CSU), said that the federal government was threatening “the ability of the German states to act with independence”.
Seehofer and his cabinet demanded that refugees be sent back before they cross the Austrian-German border.
“If the federal government does not do anything, the Free State of Bavaria will be forced to take matters into its own hands,” Bavarian Interior Minister Joachim Herrmann (CSU) threatened.
Seehofer and Herrmann would not elaborate further, with Seehofer saying only that “we will do whatever is necessary”.
Controlling the Austrian border could prove controversial, since it is monitored by the Federal Police, which answers to the federal government in Berlin, not the Bavarian government in Munich.
'Stick to Dublin rules'
The CSU politicians demanded that Berlin stick to the Dublin protocols, whereby asylum seekers are registered in the European country in which they first entered the EU.
In August the federal government decided to stop sending refugees from Syria back to their point of entry into the EU – normally Greece or Italy – and this rule has been de facto applied to all refugees in recent weeks, as tens of thousands have entered Germany from countries across several war-torn countries, including Afghanistan and Eritrea.
Merkel said on Wednesday in her joint speech to the European Parliament with French President Francois Hollande that the Dublin rules were now “obsolete”.
Seehofer also called for the government to make it a priority that registration centres which have been agreed upon by the EU be set up in Greece and Italy by November.
Lastly he demanded that limits be set on the number of family members of refugees travelling to reunite with husbands or wives in Germany at a later stage.
Austria angered by Seehofer
Seehofer had earlier threatened in an interview with Bild to start turning refugees back at the Austrian border.
"We need to take emergency measures to stem the flow of refugees, for example turning them back at the Austrian border or sending asylum seekers immediately on into other German states," Seehofer said.
But he did not go into details of how such a policy would work.
Austria reacted with immediate anger to Seehofer's comments.
"If Bavaria starts to slow down the flow of refugees and to put more controls in place, then Austria will be forced to take similar measures," Austrian Interior Minister Johanna Mikl-Leitner said in Luxembourg on Thursday.
Bavaria for its part has expressed anger that Austria allows refugees to travel unopposed into the southern German state, meaning thousands arrive daily.
The Bavarian leader's comments are also likely to bring him into further conflict with Merkel.
The two leaders of Germany's "Union" of conservative parties have repeatedly expressed opposing views on the refugee crisis in recent weeks.
Speaking in Wuppertal on Thursday, Merkel again reassured supporters that she would make a success of the crisis, but that "until then it will require a huge level of national commitment".