The Christian Social Union, which has enjoyed six decades of dominance in the state, is predicted to suffer heavy losses in the vote on 14 October.
The party is part of Germany’s grand coalition with its sister party, Ms Merkel’s Christian Democrats (CD) and the centre-left Social Democrats (SDP).
A Forschungsgruppe Wahlen poll predicted the CSU could lose up to 14 percentage points in the upcoming elections as voters flock to the pro-immigration Greens.
Support for the CSU stood at 34 per cent, compared to the 48 per cent it won in the last regional election in 2013.
The Greens appear poised to overtake the Social Democrats (SPD) to become Bavaria’s second-largest party, with up to 19 per cent of the vote, an increase of 10 percentage points since the last elections.
If the polls are correct, the Greens could become a potential coalition partner for the CSU in Bavaria.
The polls also showed the anti-immigration Alternative for Germany (AfD) party on 11 per cent, which would be enough to enter the Bavarian state parliament for the first time.
Bavaria is an important voting ground as it is the largest state and one of the richest in Germany.
The southern state is home to BMW, Siemens and Allianz and its gross domestic product is bigger than Sweden’s.
Greg Fuzesi, an economist at JPMorgan told CNBC that the upcoming Bavarian elections will “set the tone for further CDU-CSU cooperation at the federal level and could put further pressure on Merkel herself”.
”A test could come at the CDU party conference in December, when Merkel is likely to stand for re-election as leader of the CDU,” he added.
“At this stage, it is unlikely any high-profile candidate would run against her, but this will be another test of her authority."
The recent polls for the Bavarian elections also chime with the results of national surveys of voting intention.
Ms Merkel's conservative CDU/CSU bloc and the SPD each saw their voter share fall by 3 percentage points, to 26 and 15 percent respectively, the DeutschlandTrend survey for broadcaster ARD showed.
They were the monthly survey's weakest ever figures for the coalition parties, ARD said.
The poll also relegated the SPD to fourth place, behind the Greens, up 3 percentage points on 17 per cent, and the AfD unchanged on 16 per cent.
Green leaders say that voters appreciate the party’s clear stance on central issues, with an emphasis on fighting climate change and a largely liberal approach to migration.
The party is also a partner with parties from the centre-right to the hard left in nine of Germany's 16 state governments.
The Greens' election slogan in Bavaria is “Give courage instead of spreading fear.”
Green Party co-leader Robert Habeck recently spoke of the “brutalisation of political discourse.”
"We think the only way of answering that is to no longer let ourselves be driven by fear of making mistakes or by fear of AfD,“ he added.
In contrast, CSU leaders have lurched to the right in response to gains of the far-right party Alternative for Germany (AfD) before changing course in an attempt to reclaim the centre ground.
Both Bavaria’s governor Markus Soeder and the leader of the CSU Horst Seehofer made impassioned speeches to their supporters, calling for measures restrict the influx of refugees and migrants into the country.
“Those who are not entitled to protection have to return to their countries of origin, because ... no country on this planet can take in unlimited numbers of refugees and migrants,” Mr Seehofer told hundreds of delegates at the CSU party congress in September.
In July, Ms Merkel faced one of the biggest crises of her time in office when Mr Seehofer, who is also Germany’s interior minister, tendered his resignation over her migration policy.
However, the chancellor was able to strike a deal with Mr Seehofer preventing the collapse of her government.
The coalition is also embroiled in a row over how to phase out polluting diesel cars.
Additional reporting by Reuters
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