The talks come a day after Merkel vowed zero tolerance for "vile" anti-migrant violence in Germany, and amid growing criticism of the European Union's failure to agree a joint response.
Countries taking part include Macedonia and Serbia, two major transit nations for the thousands of migrants and refugees trying to enter the EU by taking the so-called "western Balkans route".
The foreign ministers of both countries called for a concerted EU action plan at the start of the summit.
"Unless we have a European answer to this crisis... no one should be under any illusion that this will be solved," Macedonia's Nikola Poposki said.
Meanwhile EU member state Hungary, which is a member of the EU's passport-free Schengen zone and has become the bloc's main entry point for migrants arriving by land along the Balkans route, was not attending the meeting.
The daily number of people crossing into Hungary hit a new high on Wednesday, topping 3,000, including nearly 700 children, police figures showed. Hungarian lawmakers will debate next week whether to deploy troops to stem the influx.
Alarmed by the growing humanitarian disaster, United Nations chief Ban Ki-moon has urged countries "in Europe and elsewhere to prove their compassion and do much more to bring an end to the crisis".
UN refugee chief Antonio Guterres and French Interior Minister Bernard Cazeneuve meanwhile have called for the urgent creation of more so-called "hotspots" -- processing centres to sort refugees fleeing war, from economic migrants simply in search of a better life.
Lack of common vision
Originally meant to focus on EU enlargement, the Balkans summit in Vienna has been hijacked by what organisers have described as "the migrant challenge".
Ahead of the conference, Austria's Foreign Minister Sebastian Kurz warned that his country would consider introducing tougher anti-migration measures including "much tighter border controls", if the EU failed to come up with a unified response.
"Austria has more migrants than Italy and Greece combined... so we shouldn't pretend that only Italy and Greece are affected," he said in an interview with public broadcaster ORF.
With no common European response, governments have approached the problem in various ways.
While Hungary's conservative government is building a 175-kilometre (110-mile) razor-wire barrier to keep migrants out -- a decision slammed by neighbour Serbia -- Czech deputy prime minister Andrej Babis has called for the EU's visa-free Schengen zone to be closed with the help of NATO troops.
Meanwhile Germany, which is preparing to receive a record 800,000 asylum-seekers this year, has eased the asylum application procedure for Syrians fleeing the country's brutal civil war.
But Berlin's largesse has not been welcomed by everyone at home, particularly in the east where a spate of attacks has targeted refugee centres.
On her visit to a migrant shelter in the eastern town of Heidenau Wednesday, Merkel was greeted by about 200 protesters, some booing and shouting "traitor, traitor".
But the German leader, who continues to enjoy strong public support, vowed: "There will be no tolerance of those who question the dignity of other people."
'Some hate us'
Also on Wednesday, violence briefly erupted in Hungary's border town of Roszke as police fired tear gas at migrants who were trying to leave a refugee processing centre after refusing to be fingerprinted.
Syrians, Afghans and Pakistanis are among those rushing to reach Hungary before the border is sealed.
"Some people hate us, they look at us in a disgusted way," a 22-year-old Syrian man told AFP at the Hungarian border.
He said he had fled the war-torn city of Aleppo and travelled through "four or five different countries".
"It makes us feel sad. You know when you walk like that, your clothes will be dirty but that's not what we usually look like."
The situation is also worsening on Europe's southern shores where rescuers found at least 55 corpses on stricken boats in the Mediterranean on Wednesday, a day that saw some 3,000 others rescued at sea.
Almost all the victims were found in the hold of a boat found drifting off the Libyan coast by a Swedish vessel. Media reports said they had choked to death on gas fumes.
The gruesome discovery adds to a toll of more than 2,300 people who have drowned while attempting the perilous sea crossing since the beginning 2015.
The latest figures already exceed the death toll for the whole of 2014, according to the International Organisation for Migration.