Merkel now faces a risky mutiny from her hardline Bavarian Interior Minister Horst Seehofer, who has vowed to defy her and order police to shut German borders to most asylum seekers by early July absent an European Union accord.
As of last week, it looked like the interior minister would go ahead with these plans with or without the Chancellor's support, potentially forcing her to sack him and thus break the three-month old coalition keeping her government together.
Senator Kamala Harris of California, was the first to do so, saying in a statement: "The Department's lack of transparency under Secretary Nielsen's leadership combined with her record of misleading statements including yesterday's denial that the Administration even had a policy of separating children at the border, are disqualifying. This will also have repercussions for Merkel's ability to move forward on euro area reforms as both CDU and CSU are reluctant to back proposals on budget lines for investment and/ or support in case of asymmetric shocks for individual member states". The CSU has governed Bavaria since 1957.
Merkel does not have many options for how to resolve the conflict.
In this Wednesday, June 13, 2018 photo, German Chancellor Angela Merkel, right, talks to Interior Minister Horst Seehofer, left, prior to the weekly cabinet meeting at the chancellery in Berlin.
But she reiterated her opposition to Germany unilaterally closing its borders as this would pass the migrant burden on to neighbouring countries, "unleashing undesired domino effects".
Hungarian Prime Minister Viktor Orban, an anti-migration hardliner, was invited to CSU meetings.
"We are convinced that Germany needs a reversal in its asylum policy", said Markus Soder, a member of Seehofer's party and the governor of Bavaria.
Merkel now faces the challenge of persuading European Union governments to sign up to a common plan on migrants. It would also gravely weaken the CSU, whose dominance of Bavarian politics relies on its influence in Berlin.
On the home front Trump has repeatedly said he wants the separations to end, but has laid blame with Democrats, the minority party in Congress, accusing them of blocking legislation on the broader issue of illegal immigration.
But Merkel says Seehofer's unilateral measure would leave countries at the EU's southern periphery alone to deal with the influx. Her government toughened asylum rules and declared several countries "safe", meaning people from there can't expect to get refuge in Germany. "A much faster turnaround on asylum seekers", Kelly told National Public Radio during a controversial interview in which he argued that undocumented migrants would not be able to easily assimilate into American society because "they don't have skills".
However, Merkel has been unyielding in defending her initial decision to keep Germany's borders open, telling lawmakers earlier this month that "in an exceptional humanitarian situation, Germany behaved very responsibly".
On common defence, Merkel has said she is "favourable" to Macron's demand for a rapid reaction force dubbed the European Intervention Initiative.
Germany, the strongest economy in the 28-nation European Union, was once a leader in the fight against climate change but has fallen behind in recent years.