"We were all shaken by the horrible news that up to 50 people died… These were people coming to seek safety," Merkel said in Vienna during a conference with leaders from the western Balkans.
"This is a warning to work to resolve this problem and show solidarity.”
Police said that a vehicle was found parked on a strip of highway in Austria, with between 20 to 50 people found dead inside. Officials said those inside were likely refugees being smuggled into the country by people traffickers.
The gruesome find comes as Merkel and Balkan leaders met to discuss how to tackle together the biggest migration crisis to hit Europe since the Second World War.
"Western Balkan transit countries are facing huge challenges" dealing with tens of thousands of refugees trying to reach the EU, Merkel said. "It is our responsibility to help them."
Migrants' futures are ‘important for our country'
Merkel was not the only German leader on Thursday to comment on the tragedy in Austria and the need for better strategies for the refugee crisis. Interior Minister Thomas de Maizière expressed his dismay over the tragedy.
"I am furious and stunned that so many people suffocated because criminal traffickers making money off of people transported them in such horrendous conditions," De Maizière said at a press conference.
The interior minister was visiting the Federal Office for Migration and Refugees (BAMF) to discuss ways to support what has become a “centrally important” office in the country as Germany has estimated that 800,000 people will apply for asylum status in the country this year.
Those who are accepted to stay in the country will need jobs and ways to settle into German life, such as through language and integration classes.
De Maizière said officials must offer more German classes and support people looking for jobs.
"They are going to want to make their futures in Germany, and that is important, that helps our country," he said.
Foreign Minister Frank-Walter Steinmeier and Vice-Chancellor Sigmar Gabriel published a ten-point plan on Monday to reform the way Europe deals with refugees, which was also reproduced in French and Italian newspapers on Thursday.