They included Hungary's premier Victor Orban, scornful of Merkel's "open-door" stance, Alexis Tsipras of Greece, home to 60,000 stranded migrants, and Boyko Borisov of newly under-pressure Bulgaria.
Austrian Chancellor Christian Kern said that the aim of the talks, also attended by top EU officials, was to "accelerate" momentum towards ending Europe's worst migration crisis since 1945.
He said that this included "massively improving" the securing of the EU's outer borders, more efforts to look after refugees in the region they come from and, longer term, a "Marshall Plan" for Africa.
Last year hundreds of thousands of people, many fleeing the Syrian war, trekked up from Greece through the western Balkans northwards, particularly into Austria, Germany and Scandinavia.
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Populist parties across Europe have stoked concerns about the new arrivals to boost support, not least Alternative for Germany (AfD). On Monday Merkel said the influx could have been better handled.
In March, under pressure from Austria, Balkan countries closed their borders, and the flow has since slowed dramatically, although 100-150 still make it to Austria every day, Vienna says.
The pact may yet collapse, however, in the wake of the July 15 coup attempt in Turkey. Kern said that the EU also needed to do similar deals with countries like Egypt and Jordan.
Greece remains under severe strain, as illustrated by a huge fire at a refugee camp on the island of Lesbos on Monday.
An EU scheme to relocate migrants stuck in Greece and fellow hotspot Italy is massively behind expectations, while extra administrative assistance promised by the EU has been insufficient.