According to reports, Merkel is more interested in supporting International Monetary Fund Director Christine Lagarde as the successor of the current European Commission president, José Manuel Barroso.
Merkel and Juncker may both hail from Europe's conservative camp but the Luxembourgish politician has fallen out of favour with a number of big players, especially in Germany.
If the European Parliament elections in May hand the centre-left an advantage in the decision-making process, Merkel may be forced to back the current president of the EU legislature, Martin Schulz, from Germany's Social Democratic Party (SPD).
The history between Juncker and Merkel dates back from when the chancellor was still in the opposition. From this perspective, she witnessed the particularly close cooperation between Juncker and the former chancellor for the SPD Gerhard Schröder.
The peak of mutual trust between Juncker and Schröder and simultaneous lowpoint in the relationship between Juncker and Merkel was during summit on security policy in early 2003. It was dubbed the "praline-summit", after the chocolate producing suburb of Brussels where four European leaders met, Germany's Schröder, France's Jacques Chirac, Belgium's Guy Verhofstadt and Luxembourg's under Jean-Claude Juncker.
The discussion focused on a highly contentious proposal for a European Security and Defence Union. At the meeting, participation was only intended for those EU countries that were seriously prepared to cooperate on defence policy.
As the meeting was going on Merkel became frustrated with Juncker, who failed to brief her party, the Christian Democratic Union, on the matter, despite their political affiliation with his Christian Social People's Party. Merkel considered the defence proposals of significant importance to Germany.
During the last European election in 2009, tension between Berlin and Juncker was already apparent. Instead of EU veteran Juncker, Herman Van Rompuy, a relative unknown, was chosen to fill the new post of European Council president.
The appointment of Van Rompuy, along with High Representative Catherine Ashton, was seen as a "double-nobody" solution for the two new political roles.
At the time, Luxembourgers were left unsatisfied by the justification given for the surprise appointment.
Diplomats mused at the time that it was a good feeling to have a big neighbour with a guilty conscience. But it seems that the guilt has not endured. "May his friends protect him", a German government source said regarding Juncker's ambitions.