Cristiano Ronaldo again was left out of the Portugal squad on Thursday, this time for games against Poland and Scotland later this month.
Santos said the Juventus forward also will not represent Portugal in games against Italy and Poland in November. Santos did not specify that the absence is related to the investigation, but he defended the character of his star player.
"[Federation] president Fernando Gomes and I spoke with Cristiano Ronaldo and we considered it best for the player not to be included in this and November's call-ups," Santos said in a news conference on Thursday.
"I personally always support my players, and this is not even a question of solidarity, but I believe what the player said publicly. He considers rape to be an abominable crime and clearly reaffirms that he is innocent of what he is being accused of. I know Cristiano well and I fully believe he would not commit a crime like that."
Santos said he spoke with Ronaldo since the allegations surfaced last week, but said "it was a personal conversation and I'm not going to make public what I spoke about with Ronaldo."
On Thursday, Nike, which has had a contract with Ronaldo since 2003, said in a statement: "We are deeply concerned by the disturbing allegations and will continue to closely monitor the situation."
Ronaldo is also the face of the EA Sports FIFA video game franchise, appearing on the cover of the 2019 game that was released worldwide last week.
"We have seen the concerning report that details allegations against Cristiano Ronaldo," EA Sports told the AP. "We are closely monitoring the situation, as we expect cover athletes and ambassadors to conduct themselves in a manner that is consistent with EA's values."
Gomes said at the news conference that he also believes Ronaldo is innocent of the allegations.
"In my name and that of the Portuguese football federation, I express my complete solidarity for Cristiano Ronaldo at a time when his good name and reputation is being called into question," Gomes said. "I believe in the words he issued [on Wednesday], not only because I defend the presumption of innocence as the basic principle of a state of law, but also because I have known Ronaldo for many years and I am a witness of his good character."
Kathryn Mayorga has filed a civil lawsuit against Ronaldo alleging that he raped her in a Las Vegas penthouse suite nine years ago. Her attorney, Leslie Stovall, said in a news conference on Wednesday that Mayorga is still in "active therapy" to deal with the emotional impact of the alleged assault.
Ronaldo has made 154 appearances for Portugal and is their all-time top scorer. Portugal travel to Chorzow to face Poland on Oct. 11 in the UEFA Nations League before taking on Scotland three days later in a friendly in Glasgow.
Ronaldo, who has scored three goals and set up four others in seven Serie A starts for Juve, has not featured for the national team since Portugal's round of 16 World Cup defeat against Uruguay. He was rested in the 1-1 friendly draw with Croatia and the 1-0 win over Italy in the Nations League last month to be given time to adapt to Serie A following his €100 million transfer from Real Madrid in the summer.
Ronaldo missed Juventus' Champions League win against Young Boys on Tuesday after serving a one-match ban for receiving a red card in Juventus' victory over Valencia.
"In the future, nothing is going to stop Ronaldo from being in the squad," Santos said. "He has always been available to represent Portugal."
Juventus issued two statements via Twitter on Thursday reiterating their support for their player.
Portugal's 25-man squad:
Goalkeepers: Beto (Goztepe), Claudio Ramos (Tondela), Rui Patricio (Wolverhampton Wanderers)
Defenders: Cedric Soares (Southampton), Joao Cancelo (Juventus), Kevin Rodrigues (Real Sociedad), Luis Neto (Zenit St. Petersburg), Mario Rui (Napoli), Pedro Mendes (Montpellier), Pepe (Besiktas), Ruben Dias (Benfica)
Midfielders: Bruno Fernandes (Sporting Lisbon), Danilo Pereira (Porto), Gedson Fernandes (Benfica), Pizzi (Benfica), Renato Sanches (Bayern Munich), Ruben Neves (Wolverhampton Wanderers), Sergio Oliveira (Porto), William Carvalho (Real Betis)
Forwards: Andre Silva (Sevilla), Bernardo Silva (Manchester City), Bruma (RB Leipzig), Eder (Lokomotiv Moscow), Goncalo Guedes (Valencia), Helder Costa (Wolverhampton Wanderers).