Merkel's allies should remember their Christian roots and show a sense of responsibility towards the poor and weak, said head of Catholic Church in Germany.
People present said he had earlier warned he would "go it alone" if allies, notably Germany, did not make vast increases in their defence budgets for next year.
US President Donald Trump will hold a one-on-one meeting with German Chancellor Angela Merkel at the NATO summit.
US President Donald Trump threatened last month to impose a 20% import tariff on all EU-assembled vehicles, part of a tough line on trade that has raised tensions across the world.
At stake is whether the UK government can devise a coherent and unified position that negotiators can then present to their EU counterparts.
Merkel struck a deal this week with her Bavarian allies to limit migrant entries through the border with Austria but she still needs to secure support from her Social Democrat (SPD) junior coalition partners.
Migrant arrivals peaked in 2015 at more than a million people, many of them fleeing the Syrian war and therefore entitled to asylum, while others were trying to escape poverty.
Germany's political crisis is the latest sign of a growing divide across the EU between those who want to maintain open borders and those who want to restrict the number of migrants entering the bloc.
While the euro initially rose to as high as US$1.1698 in a knee-jerk reaction to the news, it quickly lost steam as Seehofer's departure would be seen as making Merkel's future even more uncertain.
In a document sent to leaders of her coalition partners, Merkel listed 14 countries which had agreed to take back migrants.
The leaders of Spain, Greece, Finland and Luxembourg all expressed support for Merkel's push to curtail "secondary migration" of refugees who arrive at the EU's southern border before heading north to Germany.
German newspapers fused the fates of German team coach Joachim Loew and Chancellor Angela Merkel who, after 12-1/2 years looking unassailable, is fighting for her political survival due to a row over migration with her Bavarian allies.
If she fails to secure bilateral deals and show progress is being made to deal with the influx of migrants who have entered Europe, she will return to Berlin a lame duck chancellor, or possibly even out of a job.
A potential failure to stem the flows of asylum-seekers into Germany raises the possibility of a mutiny by Merkel’s Bavarian coalition partners.
There is a corner of Berlin where the golden age of US-German relations lingers on.
Statistics published last month showed that overall crime fell 9.6% in Germany in 2017.
Merkel said she would seek agreement with European nations at a June 28-29 EU summit, but stressed there was "no automatism" about rejecting asylum seekers if no deals are reached.
She insists that unilateral action by Germany would trigger a wider crisis, and will now use the run-up to a June 28-29 summit of EU leaders to try and forge some sort of agreement.
At a regular meeting of their joint Cabinets on Tuesday, Germany will seek the support of French President Emmanuel Macron to find a common EU response for managing an influx of refugees.
German Chancellor Angela Merkel said she favours a US-Russian summit, seeking to push global diplomacy forward after a tumultuous meeting of Group of Seven leaders.
The summit did not mark the end of the transatlantic partnership between Europe and the US, Merkel said. But she repeated that Europe could no longer rely on its ally and should take its fate into its own hands.
Merkel said that the bailout fund, know as the European Stability Mechanism (ESM), was not sufficient to shield the euro zone from crisis.
French President Emmanuel Macron heads to Berlin Thursday for talks with Chancellor Angela Merkel, hoping to breathe fresh life into his grand vision for EU reforms in the face of growing German resistance.
Less than a year after his stunning election win on a pro-EU platform, Macron's hopes of pushing through his bold post-Brexit reforms with Chancellor Angela Merkel by his side are facing a cold dose of reality.