RFEF president Rubiales has been widely condemned for kissing Spain women's star Jenni Hermoso during the medal and trophy presentation ceremony after the Women's World Cup final, but has insisted it was "consensual" while refusing to step down from his position.
Hermoso has since clarified that she did not consentto the kiss, which has led to Spanish prosecutors opening a criminal investigation into the president.
Rubiales has beensuspended for 90 days by FIFA, and the Commission of Presidents of Regional and Territorial Federations of the RFEF have now deemed his behaviour as "unacceptable" while calling for his resignation and a "restructuring in strategic positions".
"After the latest events and the unacceptable behaviours that have seriously damaged the image of Spanish football, the presidents request that Mr. Luis Rubiales immediately present his resignation as president of the RFEF," an official statement from the governing body reads.
"We will urge the corresponding bodies to carry out a deep and imminent organic restructuring in strategic positions of the Federation to give way to a new stage of management in Spanish football."
It has also been revealed that theRFEF sent UEFA a letter requesting for their teams to be expelled from European competitiondue to government involvement - but it was rejected.
Meanwhile, Rubiales' mother has gone on hunger strike at a church in Motrilbecause of what she described as an "inhuman hunt" against her son.
Rubiales finds himself further cornered after his close friend and Spanish women's national team coachJorge Vilda also criticised him.