The fears mean Angela Merkel’s sister party could be overruled in the vital Bavarian election, as anti-immigration Alternative for Germany (AfD) gains consensus with nearly half voters citing refugees as their main worry, polls show.
The ruling Christian Social Union (CSU) looked unrivalled following the 2013 election in Bavaria, when it won an absolute majority.
But the most recent poll from pollster Bayertrend reveals the party hit a record low this month, just weeks ahead of the vote, scheduled for October 14.
The survey, which analysed the voting intention of 1,000 people in Bavaria between September 5-10, shows voters fleeing the centre-right and increasingly supporting populist AfD.
According to the Bayertrend poll, just 35 percent of the surveyed are thinking to vote for the CSU, the Bavarian counterpart of Ms Merkel Christian Democratic Union (CDU).
The loss of confidence in the CSU is staggering if compared to the results achieved in 2013, when the party won 47.7 percent of seats.
The poll shows also the centre-left SPD losing votes, going from 20.6 percent to 11.
In turn, 11 percent of those polled said they will support AfD.
The far-right party, which has starkly criticised Ms Merkel’s open border policy, was founded in 2013.
While winning the 35 percent of seats in the Bavaria parliament would still make the CSU the biggest party in the state, it would deal a hard blow to the party’s leadership, indicating the policies adopted haven’t been supported by voters.
Another survey from Bayertrend says the trigger for discontent among voters is immigration.
The poll reveals 44 percent of Bavarians believe refugees to be the main challenge faced by their state.
Housing and education came in second and third position, with respectively 22 and 19 percent of votes.
Bavaria, one of Germany’s wealthiest regions, home of BMW and Siemens, is one of the country’s areas that have seen more arrivals since 2015.
The southern border has become, since the beginning of the refugee crisis that saw 1.4million immigrants reaching Germany, the favourite point for refugees to enter the country.
Mr Seehofer put up a harsh fight against his government’s ally Ms Merkel earlier this year, taking a hard line on immigration.
Their tug of war focused on the right of police officers to turn back immigrants at the border without letting them entering the country.
While Mr Seehofer deemed this move essential to cut the numbers of arrivals and bureaucracy, the Chancellor feared it could antagonise EU leaders, as it would go against Brussels’ immigration policies.
This dispute nearly brought down the governing coalition, which sees CSU, CDU and SPD sharing the power in the Bundestag.
But in June the pair struck a compromise, establishing so-called transit zones along Germany’s southern border to allow for accelerated deportations of refugees who are not entitled to seek asylum in the country.
Ms Merkel said: “After a hard struggle and difficult days, this is a good compromise, allowing us to preserve the spirit of partnership in the EU.”
But in Bavaria the deal wasn’t welcomed, and it undermined the leadership of Mr Seehofer.
A collapse in support for the CSU could lead to a reshuffling of the party’s leadership – which will have direct consequences in Berlin, with Ms Merkel risking to lose key ministers.