A Spanish court rejected a request from the Brazilian footballer to be released on remand as the probe continues over the alleged assault in a Barcelona nightclub.
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Alves has always denied any wrongdoing after the woman in question filed a complaint last month.
Alves' lawyer had asked for him to be released on bail providing he surrendered his passport and wore an electronic tag.
But the request was turned down and the court ordered the former Barcelona, Juventus and Paris Saint-Germain defender to remain at the Brians 2 prison near Barcelona.
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The court ruled that Alves was a flight risk and must remain in prison during the investigation.
The court said: "There is a high risk of fleeing as the severe punishment he faces in the present case, the strong evidence of wrongdoing and his economic might would make it possible for him to leave Spain at any time."
Alves was detained in January after accusations from the woman came to light about an incident at a nightclub on December 30, to which Alves claimed sex with the accuser was consensual.
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The star's defence team said: "Daniel Alves remains as innocent as he was before this ruling. His desire to leave Spain and elude the process did not, and does not, exist."
In Spain, a claim of rape is investigated under the accusation of sexual assault, carrying a jail term of four to 15 years.
Conviction can also lead to financial compensation to be paid to the victim to cover physical, physiological and moral harm.