The Christian Social Union took 37.2 per cent of the vote, down from 47.7 per cent five years ago.

It was the party's worst performance since 1950 in a state vote in Bavaria, which it has traditionally dominated.

Constant squabbling in Merkel's national government and a power struggle at home have weighed on the CSU.

It is traditionally a touch more right-wing than the chancellor's party and has taken a hard-line on migration, clashing with Merkel on the issue.

There were gains for parties to its left and right.

The Greens won 17.5 per cent to secure second place, double their support in 2013. The far-right Alternative for Germany, or AfD, entered the state legislature with 10.2 per cent of the vote.

Meanwhile, the centre-left Social Democrats, Merkel's other national coalition partner in Berlin, finished in fifth place with a disastrous 9.7 per cent, less than half what they received in 2013 and their worst in the state since World War II.

The CSU has governed Bavaria, the prosperous southeastern state that is home to some 13 million of Germany's 82 million people, for more than six decades.

Needing coalition partners to govern is itself a major setback for the party, which exists only in Bavaria and held an absolute majority in the state parliament for all but five of the past 56 years.

"Of course this isn't an easy day for the CSU," the state's governor, Markus Soeder, told supporters in Munich, adding that the party accepted the "painful" result "with humility".

Pointing to goings-on in Berlin, Soeder said, "It's not so easy to uncouple yourself from the national trend completely."

Still, he stressed that the CSU emerged as the state's strongest party with a mandate to form the next Bavarian government.

Australian Associated Press