Ms Kramp-Karrenbauer is aiming to give up leadership of the CDU in the summer. Party insiders said she wanted to "organise the process of the chancellor candidacy during summer, prepare the party for the future and then hand over the party chair". But the CDU source revealed Angela Merkel wants Ms Kramp-Karrenbauer to remain as a party minister.
Minister of State Michael Roth tweeted: "The shocks continue," and added "it becomes even more uncertain whether decent democrats and bipartisans stand together in the fight for democracy & against nationalism. Disturbing."
Left party leader Katja Kipping has expressed fears that the CDU will now move towards a Government coalition with the AfD.
"AKK's merit was that she kept the boundary between the Union and the right, thereby preserving the Union's soul.
"The fight for AKK's successor will be a directional debate."
She added if this ends up being Friedrich Merz, "then the CDU will soon form a coalition with the AfD".
CDU leader Ms Kramp-Karrenbauer had been favourite to succeed Mrs Merkel when she stands down next year.
Mrs Merkel has been Chancellor since 2005 but her fourth consecutive term is due to end in December 2021.
But Ms Kramp-Karrenbauer said this morning in a party meeting there was an unresolved relationship between parts of the CDU with the AfD and the Left.
She is strictly against cooperation with these parties.
Ms Kramp-Karrenbauer also claimed it is obvious party presidency and chancellorship or the candidacy for chancellorship belong in one hand.
This marks the latest blow to German politics in what has been a chaotic year for the country.
Ms Kramp-Karrenbauer won a vote in December 2018 to succeed Mrs Merkel as CDU leader.
But she has been struggling to assert her control over her conservative party after a regional branch defied her by backing a local leader helped into office by the far right.
The controversy occurred in the eastern German state, Thuringia, when Bodo Ramelow, the leader of the state, was toppled by a political collaboration which drew together the far-right AfD and the CDU.
Mr Ramelow’s Die Linke party was victorious in Thuringia’s state elections last year, and the party recently agreed to a coalition deal.
However, in a shock political manoeuvre, Mr Ramelow then lost the vote for state premier as the AfD backed another candidate.
It was widely expected Mr Ramelow would be re-elected with ease to form a minority government in the third round of voting.
Instead, underdog candidate Thomas Kemmerich of the Free Democratic Party clinched a small victory of 45 votes to 44.
Ms Kramp-Karrenbauer said local CDU politicians acted directly “against her will” in backing Mr Kemmerich, and the party chief vowed to push for snap elections to resolve the matter.
It marked the first time the AfD had played a role in forming a government in Germany.
German Chancellor Mrs Merkel branded the election “unforgivable”.
She called the vote a “bad day for democracy” and said it should be reversed.
Speaking during a visit to South Africa shortly after the results were announced, Mrs Merkel condemned the vote by MPs.
The Chancellor said: “It was a bad day for democracy, a day that broke with the long and proud tradition of the CDU’s values.
But in a speech at the party congress, Ms Kramp-Karrenbauer issued an ultimatum to her opponents..
She told delegates: "If you are of the opinion that the Germany I want is not the one you want,then let's end it. Here, now and today.
"But, dear friends, if you want this Germany, if you want to take this path together... then let's roll up our sleeves here and now and make a start."
Mrs Merkel also gave a speech at the party congress, calling for unity within the CDU.