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.
Speaking at a Monday briefing, the key Merkel ally and Christian Social Union (CSU) party head said that the chancellor effectively approved nearly all provisions of his so-called "master plan".
The leaders of Germany and France agreed Tuesday to create a Eurozone budget they hope will boost investment and provide a safety mechanism for the 19 nations using the euro currency, and also to seek a European solution to migration issues.
Seehofer, who heads one of three parties in Merkel's coalition, defied the chancellor with plans to order migrants turned away from Germany's borders as soon as Monday.
Merkel and Macron have both stressed that, as US President Donald Trump openly challenges the European Union with a trade war and over security and climate policy, the bloc must learn to stand its ground on the world stage.
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Seehofer leads the Bavarian conservative party, the Christian Social Union, the sister party to Merkel's Christian Democratic Union and a crucial coalition partner. When she finally gave a reply several weeks ago, it fell short of many of Macron's core demands.
German Chancellor Angela Merkel at the CDU headquarters on September 25, 2017.
"These points are for the French government, the president, non-negotiable, they must be present in the Franco-German euro zone roadmap, otherwise the entire euro zone will be weakened".
The Bavarian party wants to tighten rules governing the entry into Germany of migrants who are first registered in another European Union country and those rejected for asylum.
The leaders of Germany and France have announced plans on Tuesday to strengthen the European Union's (EU) capabilities in addressing worldwide security challenges and the refugee crisis, APA reports quoting Anadolu Agency. Seehofer - then the governor of Bavaria, where most migrants first entered Germany - became a leading critic of her welcoming approach.
The CSU exists only in Bavaria, and the CDU in Germany's other 15 states.
NELSON: The interior minister and his party, which is facing a major challenge from far-right populists in upcoming regional elections, say they will unilaterally prevent migrants from crossing Bavaria's global borders if Berlin doesn't act.
Seehofer and Merkel have long had an awkward relationship.
The number of applications for asylum in Germany dropped by 70 percent in 2017 compared to the previous year but Germany remains the main target for asylum seekers in the EU.
A populist-far right government in place in Italy, as well as the conservative-far right in power in neighbouring Austria, have also taken an uncompromising stance on immigration.
European Commission President Jean-Claude Juncker said it was "not the American president's role to speculate - as he did yesterday - that the German people would march towards the chancellery to remove Mrs Merkel".
The office said in an annual report that 728,470 application requests were made for global protection in 2017, compared with nearly 1.3 million applications the previous year.