But by Sunday evening it was looking as though she had bested one of her harshest critics on migration, Horst Seehofer, the head of Merkel's Bavarian sister party, the Christian Social Union, and her current interior minister.
A folksy master of Bavaria's conservative beer hall politics, Horst Seehofer has become the most unsafe critic of Chancellor Angela Merkel's immigration policies and the man who could end her reign.
According to summit conclusions, European Union member states will, on a voluntary basis, set up so-called "controlled centers" to host and transfer migrants that landed on European Union shores.
The Social Democrats, who have largely been bystanders so far, demanded that their coalition partners get their act together, and called for a meeting later Monday with the conservative leaders.
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A relieved-looking Merkel, who has been in power since 2005, emerged from the late-night negotiations hailing a "very good compromise" that would "control" new arrivals of migrants and asylum seekers while upholding European Union co-operation and values.
Mr. Seehofer, who remains as leader of the CSU, can argue that even though he compromised in the end he pushed the chancellor to act on an issue that has eroded his party's support in Bavaria.
The centre-left Social Democrats, another partner in the coalition, must also accept the deal along with neighbouring Austria.
To resounding laughter across the chamber he said: "I believe you would have smilingly deported Jesus".
Ms Merkel has emerged from the row severely damaged. Leaders of five countries considered possible locations of refugee camps outside the EU - Egypt, Albania, Morocco, Tunisia and Algeria - have said they are not interested in any such deal with the EU.
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Seehofer is due to travel to Austria on Thursday in an attempt to hammer out a deal with the Austrian chancellor, Sebastian Kurz.
He urged Merkel to block asylum-seekers at the border if they have no identification papers or if they had already registered in another European country, The New York Times reported. Party leader Andrea Nahles said "the CSU is on a unsafe ego trip that is paralyzing Germany and Europe". Austrians, for instance, will not be willing to accommodate refugees and will therefore close their border with Italy and Slovenia quite soon, he explains.
"It was a mistake that will follow us for a long time", he said at the time.
Nevertheless, the anti-refugee, anti-Islam Alternative for Germany (AfD) was propelled into federal parliament for the first time previous year by outrage over immigration, leading to months of paralysis while Merkel struggled to put together a workable coalition.
The idea of setting up centers at the border with Austria to process migrants is not new.
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A real possibility is a break up of the 70-year alliance between the CSU and Merkel's CDU. About 18,000 had already applied for asylum in another European Union country.