"We want to reject what we consider to be unacceptable behaviour from Mr Rubiales, who has not lived up to the institution he represents," captain Alvaro Morata said as he read out a statement on behalf of the team.
"Spanish football should be a motor of respect, inspiration, inclusion and diversity and should set an example with its conduct both on and off the pitch."
Spain's Sport Administrative Tribunal (TAD) on Friday opened a case against Rubiales for "serious misconduct."
Rubiales' behaviour has sparked outrage in Spain and abroad.
World soccer governing body FIFA has already suspended Rubiales from all football-related activities for three months while it conducts an investigation.
Persons:
Royal Spanish Football Federation Luis Rubiales, Luis Rubiales, Jenni Hermoso, Mr Rubiales, Alvaro Morata, Morata, TAD, Rubiales, Letizia, Pietro Lombardi
Organizations:
Soccer Football, Spanish Soccer Federation, Del Futbol, Royal Spanish Football Federation, REUTERS Acquire, Rights, FIFA, Thomson
Locations:
Del Futbol Las, Rozas, Spain, Handout, Rights MADRID, Spanish