Despite having been heavily praised by the public for his handling of the state bureaucracy during the 1906 disaster, Pardee continued to have a strained relationship with the Southern Pacific Railroad, one that had been ongoing since the 1890s while he was Mayor of Oakland. Pardee's role in the burgeoning Progressive movement which distrusted large corporate monopolies, as well as his efforts to conserve and protect state forests, remained a constant thorn for Southern Pacific executives. A lengthy bitter battle over the Port of Oakland, which Pardee argued on behalf of Oakland that the port was a municipal rather than private corporation, dragged out for much of his governorship. The case was decided upon by the California Supreme Court in 1906, ruling in Oakland's favor. Pardee also encouraged creation of new railroad companies to break the Southern Pacific's monopolies.