The open confrontation between Chancellor and Seehofer lasted for a week, since Merkel prevented minister from presenting his master plan for asylum, with which he wants to expel refugees who reach German borders and whose demand for asylum has been taken in Anor union country.
In her fourth term at the helm of Europe's largest economy, Merkel made it clear that she has no intention of being pushed around after an internal power struggle over immigration escalated into a threat to her government. Crime in Germany is way up.
Seehofer threatened Monday to turn back migrants if the German leader doesn't secure a deal within two weeks.
And 86 percent want faster deportations of rejected asylum seekers, a process now often held up by bureaucratic hurdles and legal challenges, according to the Infratest dimap poll.
More than 1 million migrants came to Germany in 2015 and 2016, though numbers have since dropped sharply.
And it may also break apart a long-lasting alliance between Germany's two Christian sister parties, the CDU, led by Mrs Merkel, and its Bavarian counterpart, Mr Seehofer's CSU.
If Merkel can't reach a comprehensive solution with European Union countries in the next two weeks, the situation could quickly escalate, experts warn, possibly leading to a collapse of her coalition.
Despite increased political pressure from Berlin and Rome, talks on reforming the bloc's internal asylum rules remain stuck with southern and wealthy central states demanding that all European Union members host some of the new arrivals.More news: Trump directs Defense to create U.S. 'space force'
"The people are running out of patience", he told Bild daily.
The rules require migrants to apply for asylum in the first country they enter - a policy France has used to defend its own efforts to keep people from trying to cross over from Italy.
The ministerial retreat at Meseberg castle near Berlin aims to agree a joint Franco-German stance ahead of a key June 28-29 summit on the EU's post-Brexit future, at a time when populists and eurosceptics are rapidly gaining ground.
The CSU, which faces a regional election in Bavaria in October, has recently sharpened its criticism of Chancellor Merkel's open-door policy for refugees.
Trump announced past year that the USA will pull out of the accord negotiated by his predecessor unless he can "get a better deal".
A CSU leadership meeting Monday in Munich is likely to authorize Seehofer to go ahead with his plan - but it's unclear at what point.
Merkel is under strong pressure from her conservative allies to take a harder line on migration. Then, Merkel's coalition, which also includes the Social Democrats, would lose its parliamentary majority.
"We see somewhat positive developments there", Merkel told reporters Tuesday.
However, "the European project is at risk", and "we have a particular responsibility", she said. There are claims that Merkel's politics created the political space for the AfD.