Merkel rejected next weekend's ultimatum set by Seehofer, her conservative ally turned harsh critic, saying migrant arrivals from Syria and other crisis regions could not be immediately stopped.

"We cannot flip the switch in one go - we must proceed step by step," she told a news conference in Berlin in a further rebuff to her partner in her grand coalition federal government.

Her response followed Sunday's EU-led talks in Brussels where EU and Balkan leaders agreed to stem flows by introducing a package of measures, including establishing more refugee camps in Greece. On Tuesday evening, she was due in Paris for talks on ways to end the warfare in Syria.

Merkel unfazed by Bavarian 'self defense'

Earlier in Berlin, Merkel had not mentioned Seehofer by name nor his latest remark to the Passauer Neuen Presse newspaper that Bavaria could resort to "self defense."

Should pressure on Berlin prove unsuccessful, then Bavaria would consider options for action, Seehofer said, referring to transits of up to 11,000 refugees daily via Bavaria into Germany from Balkan routes now mainly stretching through Slovenia and Austria.

A similar Seehofer threat a fortnight ago prompted reminders from constitutional experts that border control was the prerogative of Germany's federal government, and not of its 16 regional states.

Austria 'straining neighborly relations'

Premier Seehofer, who also heads Bavaria's conservative Christian Social Union (CSU) party, also accused Austria on Tuesday of straining "neighborly relations" by transporting thousands of refugees to Bavaria's border unannounced.

"I've never experience Austria behaving like this," state interior minister Joachim Herrmann told Bavaria BR public broadcasting, accusing Vienna of only being focused on enabling the "quickest possible passage" of refugees to Bavaria.

Its actions were scandalous and irresponsible, Herrmann claimed.

Since early September, at least 318,000 people had entered Germany via Bavaria, Herrmann said after a regional cabinet meeting in Munich on Tuesday.

Consultation with Austria 'constant'

Merkel also rejected another Seehofer accusation of failing to consult Austrian Chancellor Werner Faymann by telling reporters in Berlin that her team had "almost constant daily contacts with Austria at all levels."

Austrian chancellery minister Josef Ostermayer said Faymann was in "close contact" with Merkel.

Ostermayer said similarly he was in touch with Peter Altmaier, Merkel's chancellery head and refugee crisis coordinator, to deal with the refugee situation humanely.

"Once the refugees are already on the move, it is more a matter of deciding whether we provide the people with medical care and food or we let them freeze to death,"Ostermayer said.

"In this challenging situation we must behave humanely," Ostermayer said, adding that the goal must be to register refugees on the EU's external borders.

Refugees ill as weather turns chilly

Refugees, including many children and elderly people, facing autumn weather, had been arriving via Croatia at Slovenia's border town of Brezice with respiratory illnesses and diarrhea, medics said on Tuesday.

On Monday night, hundreds were left in a no-man's-land on the Slovenian-Austrian border, according to the German news agency DPA.

Many, who were without water and food and who had lit fires to stay warm, had chanted in unison: "We want to go!"

Croatia police said on Tuesday for the first time during the crisis 1,300 migrants had been taken direct by train to the Slovenia border village of Dobova instead of being unloaded on fields close to Croatia's border with Slovenia.

The small EU nation has counted around 84,000 migrant arrivals since October 16 when Hungary sealed its border with Croatia.

Germany on Tuesday considered sending police to assist Slovenia.

ipj/ng (AP, Reuters, AFP, dpa)