Complaints over Merz's high-handed leadership style have boiled over after the personnel changes prompted by the resignation of the CDU's parliamentary leader Jens Spahn.
Spahn had to step down this month after it emerged he and his husband had had a child via a surrogate mother in the United States, despite the practice being illegal in Germany and vehemently opposed by the CDU.
CDU lawmakers will meet on Wednesday to formally elect Spahn's successor Thorsten Frei, Merz's chief of staff.
At that meeting Merz may have to face the music from lawmakers angered by the way he conducted the reshuffle, including the botched sacking of transport minister Patrick Schnieder.
Merz's intention to sack Schnieder leaked last week but the minister was left dangling in the post after Merz's initial pick for his replacement pulled out.
A CDU state secretary in the health department, Tino Sorge, meanwhile took to Facebook to say that Merz had sacked him without bothering to speak to him first, saying this was "a question of (Merz's leadership) style".
Long perceived by sections of the public as arrogant and detached from voters' concerns by virtue of his business background and private wealth, Merz is now being openly scolded by senior CDU figures for the same faults.
The head of the CDU in the northern city-state of Bremen, Heiko Strohmann, told Merz in a recent party meeting that he "was running a political party, not a business".
In contrast to a firm with employees, "the CDU depends on volunteers, on elected lawmakers, you can't boss them around," Strohmann told the Tagesspiegel newspaper on Wednesday.
Scathing opinion pieces in German newspapers have begun to ask whether Merz will be able to rebuild his standing in the party and even whether he will be able to complete his full term as chancellor.
The internal ructions are another headache for Merz, already beset by poor poll ratings for him and for the CDU, currently lagging behind the far-right Alternative for Germany (AfD).
The AfD is predicted to significantly outperform the CDU in three state elections in eastern Germany in September, which may prove another crunch point for Merz's leadership.
