The German government on Thursday said it would continue border controls at its border with Austria for six more months to ensure Germany's security and deal with ongoing illegal immigrant flows.

Interior Minister Horst Seehofer said he valued the European Union's Schengen zone of free travel as one of Europe's greatest achievements, but he had no choice but to extend the checks at the Austrian border for now.

"Deficits in protection of the EU external borders and the scale of the illegal, secondary immigration at the moment allow no other conclusion than that domestic border controls at the German-Austrian border remain necessary," Seehofer said in a statement released by the ministry.

Germany and other Schengen countries introduced emergency border controls in 2015 after more than 1 million refugees and mostly illegal immigrants flooded into Europe. Seehofer has been a frequent critic of Chancellor Angela Merkel's decision to de-facto open Europe's door to many millions.

His Bavarian CSU conservative party is scrambling to win back voters in the upcoming Bavarian state election. In the national election last September, it bled support to Alternative for Germany, which has even tougher views on immigration than Seehofer.

Seehofer had repeatedly vowed to continue the border checks during the national election campaign.

The ministry said the decision to extend the controls, which takes effect on May 12, had been coordinated with France, Austria, Denmark, Sweden and Norway. The six countries had agreed last year to extend the internal border checks until mid-May.

It said it notified other European countries about the decision on Thursday.

Nearly all EU states consider the free-travel Schengen area to be a major benefit of decades of European integration. They are keen to avoid disruptions to travel and trade.

However border checks have become the new reality since 2015 and the bloc is working on changing its laws to allow for the introduction of such measures more easily and for longer periods.

The two parties have clashed on not only the issue immigration but also German culture. Chancellor Merkel had made a now infamous statement on her 2016 new year's broadcast that "Islam belongs to Germany."

However Alexander Dobrindt, deputy party chief of the CSU, stated in an interview with Focus magazine that "Islam does not belong to Germany."

Wolfgang Schaeuble appeared to be following Merkel's lead by distancing himself from CSU leader Horst Seehofer and Dobrindt, both of whom have repeatedly emphasized that Islam is not part of Germany.

Dobrindt said that suggesting Islam belonged to Germany was "a barrier to integration" that "sends a false signal to immigrants."

Asked whether the CSU is bracing for a long-term dispute with its senior coalition partner on the issue, Dobrindt said his party was heading into the debate with a clear stance.

"The CSU will not budge on this," he said. "After all, the majority of the population is of the opinion that Islam does not belong to Germany."

The CSU gives a voice to this majority which "wants to preserve our cultural identity for the future," said Dobrindt.