The raids come after the federation was rocked by a sexism scandal after its former president kissed a player on the lips without her consent during the Women’s World Cup awards ceremony last month.
Players had reported to camp on Tuesday after being picked by new coach Montse Tomé against their will on Monday.
According to Spanish sports law, athletes are required to answer the call of their national teams unless there are circumstances that impede them from playing, such as an injury.
Prosecuting Spain football official Rubiales for World Cup kiss seems illogical, says UEFA president
Spanish state prosecutors are investigating Jenni Hermoso’s accusations against Luis Rubiales of sexual assault for the kiss at the August 20 final and coercion for then pressuring her to defend him.
In the players' new statement on Monday, they said the federation can't force them to join up with the team and said the call-up was not made in accordance with current FIFA regulations.
Spanish football has been in turmoil since Rubiales forcibly kissed midfielder Jenni Hermoso on the lips in front of the world's media after Spain defeated England in the Women's World Cup final.
Luis Rubiales arrives at Spanish court to be questioned over his kiss of player at Women's World Cup
Judge Francisco de Jorge issued the order earlier this week for Rubiales to answer his questions at Spain’s National Court.
Rubiales kissed Spanish Women's team player Jenni Hermoso following Spain's triumph in Sydney on August 20, which she says was not consensual, while Rubiales insists it was.
Rubiales sparked a worldwide backlash after forcibly kissing midfielder Hermoso during the medal ceremony following Spain's World Cup triumph in Sydney on August 20.
Spanish Football Federation president Rubiales, 46, sparked a worldwide backlash after forcibly kissing a female player during the medal ceremony following Spain's triumph in Sydney on August 20.
Spanish footballer Jenni Hermoso files sexual assault complaint against Luis Rubiales over World Cup kiss
The prosecutors’ office said that, according to a new sexual consent law passed last year, Rubiales could face a fine or a prison sentence of one to four years if found guilty.
In a letter signed by its interim president Pedro Rocha, the RFEF offered its "most sincere apologies... for the totally unacceptable behaviour of its highest institutional representative.
FIFA has already suspended Rubiales for 90 days while it carries out its disciplinary case, so the Spanish decision will have little immediate effect.
Spain men's football coach seeks forgiveness for applauding Rubiales' diatribe against 'false feminists'
De la Fuente was speaking a week after he clapped several times during an emergency general assembly of the Spanish soccer federation when Rubiales, the organization's president, refused to step down
FIFA suspended Rubiales, the vice president at European soccer body UEFA, for at least 90 days while it investigates the kiss he forced on Women’s World Cup winner Jenni Hermoso.
In a statement released by women players' union Futpro, Hermoso and 80 other players said they would not accept an international call-up "if the current leadership continues" at the RFEF.
After Spain's 1-0 win over England in the final in Sydney on Sunday Rubiales gave midfielder Jennifer Hermoso an unsolicited kiss on the lips. He also celebrated victory by grabbing his genitals.
In another incident on Sunday evening, broadcast around the world, Spanish football federation chief appeared to be grabbing his genitals with both hands to celebrate Spain's victory.
The Spanish football federation called an emergency meeting for Friday and activated an internal investigation into the incident, amid mounting pressure to take action against Rubiales.
Luis Rubiales kissed Jenni Hermoso on her lips after she collected her medal following the final in Sydney, provoking outrage in Spain.