Berlin's mayor Michael Müller had last week appointed Waltz and Swedish ballet chief Johannes Öhman as co-directors of Germany's largest ballet company from the 2019/2020 season on.
But in a scathing petition posted on the company's homepage on Sunday, the dancers said: "Unfortunately, the appointment has to be compared to an appointment of a tennis trainer as a football coach or an art museum director as an orchestral director."
They described the nomination as "disruptive and insulting to the company," and added that the fact that "this announcement comes in the middle of an election campaign leads us to believe that it is politically motivated rather than artistically."
Berlin votes Sunday in a state election, a timing the dancers find dubious as Waltz's term is due to start a whole three years from now.
Their suspicion is that Waltz, 53, is a big name who will sell tickets but as a choreographer of dance theatre lacks the background for classically-trained ballet.
Her appointment had been broadly welcomed by German media, which had been little impressed by the current director Nacho Duato, noting that none of his three premieres since he joined in 2014 had been a hit.
The Staatsballett is a merger of three companies - Deutsche Oper in west Berlin and Komische Oper and Staatsoper in the east - a legacy of a divided capital.
The conflict plaguing the dance company comes a year after a similar dispute at east Berlin's legendary theatre Volksbühne (People's Stage), over the succession of veteran artistic director Frank Castorf, who is to bow out in 2017 after a quarter-century at the helm.
Berlin authorities, which heavily subsidise the avant-garde theatre and Castorf's daring, politically-charged productions, declined to keep the strong-willed iconoclast much beyond the end of his current contract in 2016.
The director of London's Tate Modern museum, Chris Dercon, has been nominated as his replacement, but some 172 actors and employees of the theatre have written an open letter voicing their "deep concern" over the appointment.