Twenty-four out of 35 local MPs voted to oust Governor Celestin Chibalonza.
The MPs said Mr Chibalonza, from President Joesph Kabila's ruling party, had also badly managed finances and had little respect for local authorities.
Despite elections last year, the east of the country has remained unstable with rape and looting commonplace.
This month, thousands of civilians from North Kivu have fled to South Kivu after renewed fighting.
The Congolese army is struggling to quell a rebellion in North Kivu by renegade Tutsi Gen Laurent Nkunda.
In South Kivu, the army is facing a separate ethnic uprising by the Banyamulenge community, who are demanding autonomy.