German politicians and media questioned how long Angela Merkel could carry on as chancellor on Wednesday after her conservatives ditched a long-standing ally as head of the parliamentary party, defying her wishes and dealing a blow to her waning authority.

The upset, before an Oct 14 election in Bavaria in which her CSU conservative allies face heavy losses, follows the third crisis in as many months for her loveless coalition with the Social Democrats (SPD).

"Can Merkel Still be Chancellor?" splashed top-selling Bild with a photo of the 64-old pulling a grim face.

SPD lawmaker Thomas Oppermann tweeted it was an "uprising against Merkel" and Free Democrat Alexander Graf Lambsdorff said it was "the beginning of the end of the grand coalition".

In an unexpected vote that underscored growing discontent among conservative lawmakers after 13 years of Merkel as German chancellor, Volker Kauder, lost out to Ralph Brinkhaus in a secret ballot for the party post.

However, many commentators point out that Merkel's continued weakness will result in little change in terms of policy.

Lawmakers had gone against the wishes of Merkel and CSU leader Horst Seehofer who had both called on them to re-elect Kauder, a trusty lieutenant who over 13 years helped secure the support of parliamentarians in the euro- and migrant crises.

Many conservatives are still angry over Merkel's decision three years ago to let in more than a million migrants.

"The vote shows a desire for renewal," conservative premier of the state of Schleswig Holstein Daniel Guenther said. "There was clearly a certain discontent over national politics," he told broadcaster NDR.

He added that Brinkhaus wanted to give more weight to lawmakers' views in policy decisions.

Brinkhaus is not widely viewed as a rebel who wants to oust Merkel. Although he is slightly to the right of Merkel and more hawkish on financial policy, he has so far been at pains to stress he is on her side.

"I want to support her," he told public broadcaster ZDF late on Tuesday and he has also dismissed the idea of Merkel calling a vote of confidence in parliament as "nonsense". Merkel's spokesman also said she would not call a vote.

Brinkmann has specialised in budget and financial affairs and criticised generous aid packages during the euro debt crisis. He also said he wanted to strengthen social integrity.

"Much has been broken in the last three years," he told ZDF.

In her trademark no-nonsense style, Merkel said she would not 'sugarcoat' the result and that defeats were part of democracy. Only on Monday, Merkel apologised for not taking account of the public mood over the coalition's handling of a scandal over the head of Germany's domestic security service which had threatened her coalition.

However, Merkel is still largely indispensable both to her party and to the 'grand coalition'.

Holger Schmieding, economist at Berenberg said the coalition parties would not gain from bringing down Merkel and triggering early elections as the biggest winners would be the far-right Alternative for Germany (AfD) and the Greens.

"Merkel is unlikely to throw in the towel soon," he said in a note, adding that a weakened coalition "is unlikely to drive any dramatic change of policies on the national, European or international level".