Angela Merkel keeps government together after hours of emergency talks on migration crisis

Rebellious interior minister Horst Seehofer has said he will not resign

Horst Seehofer (right) had offered to resign as interior minister (AP)

Angela Merkel has struck a deal a rebellious government minister to prevent his resignation and stop her government from collapsing over migration policy.

After hours of crisis talks that stretched late into Monday night Horst Seehofer, the interior minister, announced he would not be resigning from his post after having previously offered to do so.

Mr Seehofer, from the conservative Bavarian CSU party, had wanted a harsher policy on refugees and migrants, but Ms Merkel wants migration policy to be coordinated at an EU level.

The minister had threatened to unilaterally go ahead with his new policy of sending police to the German border to turn away refugees who had registered in other EU countries – effectively challenging Ms Merkel to sack him and bring down her own administration.

“After intensive discussions between the CDU and CSU we have reached an agreement on how we can in future prevent illegal immigration on the border between Germany and Austria,” Mr Seehofer told reporters as he left the the CDU's Berlin headquarters late on Monday.

The pair agreed a compromise policy of setting up so-called “transit centres” which would allow asylum seekers who had already registered in a different EU country to be sent back to it with the agreement of that country.

The CSU and Ms Merkel’s more moderate CDU, who do not stand candidates against each other, have been inseparable allies since 1949 and the split over migration would have been a historic break in German politics.

The deal comes after Ms Merkel got the backing from MPs of both parties at a parliamentary meeting on Monday. Mr Seehofer did not attend the meeting.

The CSU, which only stands candidates in the south eastern state of Bavaria, has long had a reputation for being more conservative than the CDU which organises in the rest of Germany.

It has tried to reassert those right-wing credentials in recent months after the far-right AfD made gains in last autumn’s Bundestag elections – notably in Bavaria.

The focus on migration by the CSU comes ahead of local elections to the Bavarian regional parliament or Landtag which are due later this year, with the AfD expected to do well. Bavaria’s geographical position means it is on the overland migration route from the middle east and Balkans, traversed by many refugees and migrants taking advantage of Angela Merkel’s welcoming borders policy.

Despite a major fall in the number of refugees and migrants coming to Europe, and in particular Germany, in the last year, the issue has rocketed up the political agenda after gains for the far-right in elections across the continent.

Far-right anti-immigration parties now participate in governments in the EU core countries like Italy and Austria, with populists also in charge in eastern states like Poland and Hungary.

Austria’s government, which has said it wants to make migration policy a priority, is taking up the chair of the European Council this week, which it will hold for six months. At a summit on Thursday and Friday last week leaders agreed a raft of measures to toughen EU border policy including condemnation of NGO boats rescuing migrants drowning in the Mediterranean, the potential establishment of asylum processing centres in North Africa, and secure zone for migrants in EU countries.