Germany, Austria and Italy will hold talks on “closing” the southern migration route to Europe, said German interior Minister Horst Seehofer after he promised that the refugees will not be sent across the Bavarian border.

At a hastily arranged meeting in Vienna with the Austrian chancellor, Sebastian Kurz, Seehofer sought support from ’s southern neighbour for .

Seehofer, whose hard line on immigration has prompted weeks of conflict with the chancellor, promised that Germany would not send asylum seekers to Austria if they were turned away at the German border, although details remained unclear.

Separately, Merkel said she wanted to protect Europe’s “humanity” in dealing with migrants, spelling out her differences with Hungary’s prime minister, Viktor Orbán, at a press conference in Berlin.

Merkel’s Christian Democratic Union party reached an agreement with its sister party, Seehofer’s Christian Social Union, to set up special transit centres at the German-Austrian border to process asylum claims. Germany also wants to reach bilateral deals with and so they take back asylum seekers.

Under EU rules, the first country of arrival is responsible for processing asylum claims, a system that has put a heavy burden on Mediterranean states and triggered angry debates about what to do with people who move to other member states.

Seehofer predicted that talks with Greece and Italy about these so-called secondary movements of people would be “extremely complex and complicated”.

Austria had feared that Germany was exporting these asylum claimants, prompting Kurz to warn that he could introduce controls along the southern border.

“These national measures would of course affect Austria and would mean that we would have to take measures along our southern border,” Kurz said hours before meeting Seehofer. “We are fighting for a European solution.”

After the meeting, Kurz said “things had been cleared up now”, but acknowledged that there would be a “period of uncertainty” while Germany sought to negotiate agreements on returns with Greece and Italy.

Under pressure from the CSU, Merkel has been scrambling to get an EU-wide solution, fearing that there will be a domino effect if Germany takes unilateral action, leading to border closures across central Europe and unravelling the EU’s border-free travel zone, imposing costs on people and businesses.

Austria has been considering imposing controls at the Brenner Pass, one of Europe’s busiest transport hubs, on its southern border with Italy. If vehicles had to detour through the Gotthard tunnel in Switzerland, Austrian officials estimate it would add €124 (£110) to the cost of each journey.

Austria, which took over the EU’s rotating presidency on 1 July, wants to strengthen the EU’s external borders while avoiding internal controls on the continent.

Kurz said “major progress” on external borders had been made at a recent summit in Brussels of EU leaders as he sought to dispel doubts about the vague communique that was agreed.

After all-night talks, EU leaders agreed that unspecified non-EU countries should host migrant-processing centres to try to prevent people risking their lives making dangerous sea crossings to Europe. Kurz said he was “convinced there are countries that are willing to work with us in the spirit of partnership”, though he did not name them.

Under Kurz’s leadership, the Austrian People’s party entered into a coalition with the far-right anti-immigrant Freedom party last December. That coalition, backed by Denmark, recently called for failed asylum seekers to be expelled from the EU to camps in the Balkans.

Diplomatic convention requires the holder of the EU presidency not to push pet projects but to act as an honest broker for all EU countries. Kurz indicated it would not be possible to push the idea of camps in non-EU countries during the next six months.

“To be honest, I do not want to elaborate on this idea because we do not want to endanger it,” he said, adding it was “not connected to the Austrian presidency but it might serve as an example for others”.

Austria has become an enthusiastic supporter of a long-standing effort by the European commission to create a European border and coastguard agency, in contrast to the policy of previous Austrian governments. Kurz called for the agency to have 10,000 border guards by 2020, seven years earlier than anticipated by Brussels.