German chancellor Angela Merkel defended the deal on transit zones reached with her rebellious sister party on Sunday and said her coalition partners needed to be convinced of it.

Merkel also warned against military presence in the Balkans, in case borders close on the migration route.

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Speaking to supporters of her conservative Christian Democrats (CDU) in the western city of Darmstadt on Monday evening, Merkel said the Social Democrats (SPD) need to support the transit zones.

Merkel's open-door policy towards refugees has created tensions within her ruling coalition that threaten the stability of the government.

She struck a deal on Sunday with Bavarian premier and CSU leader Horst Seehofer, who is pushing for so-called transit zones along the border to make it easer to filter economic migrants and people in genuine need of protection.

SPD opposes the idea of large centres along the border, where migrants will be detained.

"We continue to negotiate. It is not the first time that we have to convince the SPD of reasonable things," she told the 2000-strong crowd in Darmstadt.

"Germany will help all people who are looking for protection from wars and persecution," she said, adding that it is just as important to return people who came for economic reasons to Germany.

"The creation of transit zones for quick decisions is therefore the right way," she said.

Merkel made it clear that she sees transit zones as a political alternative to closing the border with Austria, something she is reluctant to do as it would unravel one of the European Union's signature achievements: border-free travel.

Yet, the refugee flow must be slowed for Germany, whose municipalities and local government can barely provide enough beds for the daily arrival of 10,000-12,000 people.

Other countries along the migration route, however, are not interested in slowing the flow, out of fear that the migrants would remain.

Borders risk wars

The embattled chancellor, who is increasingly being seen as isolated as the refugee crisis threatens her political future, warned of military conflicts in the Balkans if the borders along the migrant route to Germany were to be closed.

Looking at the results after Hungary closed its border with Serbia in September, Merkel said: "There will be disruptions."

After Hungary diverted the preferred route for migrants and refugees, people diverted towards the ex-Yugoslav republics of Serbia, Croatia and Slovenia to eventually reach Germany.

She said already high tensions among these countries prompted the recent meeting in Brussels with leaders from the region.

"Because I do not want [us to go] there again ... military conflicts," Merkel said.

On Thursday, Merkel will have to defend her deal to the CSU and convince the SPD to sign up for the plan on transit zones in a meeting with Seehofer and Social Democrat leader Sigmar Gabriel.

Merkel also said at the CDU gathering that Germany will have to conduct a much more active foreign policy.

"We're experiencing something we've never experienced before, that conflicts that appear to be far away, suddenly are here on our doorstep," Merkel told the meeting.