A key ally of German Chancellor Angela Merkel, Bavarian Premier Horst Seehofer, has now become a thorn in her side, bullying her publicly over the government’s open-door refugee policy.

Mr Seehofer late last month went as far as threatening to resort to “self-defence” measures if Dr Merkel did not put a lid on the refugee flow, implying that the massive influx raises existential issues for his Christian Social Union (CSU). 

On the surface, such concerns appear to be driven by his quest to be re-elected CSU party boss on Nov 20.  Germany expects to take in 800,000 to one million refugees this year and a substantial number of those fleeing the Middle East, Africa and eastern Europe are entering Bavaria, straining resources.

Mr Seehofer, 66, said he gets daily updates from district heads, town mayors and volunteers who are complaining they have reached their capacities.

As a result, the popularity of the CSU – which operates only in Bavaria and is a centre-right party – has fallen while the fortunes of the ultra-right populist Alternative fur Deutschland (AfD) have risen, according to a Forsa survey. AfD is pushing for tougher immigration controls.

Beyond those concerns, however, Mr Seehofer’s humble beginnings in a largely rural, staunchly Catholic region could partly explain his differences with Dr Merkel on the refugee crisis; he presents himself as someone fighting for the ordinary people of Bavaria’s society.

The son of a truck driver,  the young  Horst  earned his first wages delivering magazines. On weekends, he and younger brother Dieter did not even have the  50 pfennig fee required  to enter and watch the football games at a sports club in Ingolstadt, where he was born.

“We stood for as long as we could in front of the cashier until he allowed us in,” his brother told Sueddeutsche Zeitung daily.

The CSU headed by Mr Seehofer has long held a tough stance on immigration.  It was widely ridiculed last year when it proposed immigrants should speak German not only in public but also at home.

Certainly Mr Seehofer has no ambitions to replace Dr Merkel as chancellor.  What his  allies fear is  that, if on Nov 20 he fails short of the 95 per cent vote he got two years ago as CSU chairman, he could be dethroned by a candidate who wants to close Bavaria’s borders altogether. That would account for Mr Seehofer’s desperation to squeeze from Dr Merkel a public statement that Germany has already reached its limit and to state the maximum number of refugee arrivals.

Mr Seehofer did not get one on Oct 31.  But Dr Merkel reversed her stance on the creation of “transit zones” for refugees, only to call them “reception centres” on Thursday following a deal with her government coalition partner, the Social Democratic Party of Germany. They will register those likely to be turned away – people from the Balkans or migrants without papers – but refugees do not have to physically remain there.

Mr Seehofer and Dr Merkel go back a long way. Then and now, their conflict boils down to differences on the extent of transformation in Germany’s society. For instance, in 2003 they clashed because he believed her plans for flat-rate contributions to the compulsory health insurance scheme benefited employers and not the employees.  Mr Seehofer lost that battle, eventually resigning as Bundestag parliamentarian in 2004.

Many thought that was his political end. But when Dr Merkel became chancellor in 2005, she put aside their differences and named him Federal Minister of Food, Agriculture and Consumer Protection. Likewise, Mr Seehofer said in a 2012 speech that his party would stand by Dr Merkel: “The CSU will be a purring kitty, not a roaring lion.”

Whether the deal on reception centres would transform him into a “kitten” remains unclear. He said on Thursday that the deal is “very, very good”. But a day later, he left open the possibility of filing a legal challenge against the government over its refugee policy.

“We’ll examine that… We will see if we will then go to court,” he said on Friday.

Bavaria officially asked former constitutional court judge Udo Di Fabio to look into the possibility of taking the government to court over Bavaria’s burdens from the refugees.

Party politics expert Tanja Boerzel of Freie Universitaet Berlin said last week’s agreement “won’t solve the problems he (Mr Seehofer) is articulating”.

“I don’t think he would simply shut up”, Prof Boerzel noted,  but said the deal could help Mr Seehofer pacify CSU members on Nov 20.