Semedo, 23, was arrested on Tuesday for his alleged involvement with others in holding a man who they threatened with a gun, according to media reports.
"The judge charged the footballer with crimes of attempted homicide, assault, threats, illegal detention, illicit possession of firearms and violent robbery," a statement from the Valencia court on Thursday read.
Semedo's agent, Catio Balde, told Portuguese television network TSF on Wednesday that his client had been tricked.
"Ruben was a victim of fraud, a large-scale swindle, probably of a financial nature. Against this situation he didn't react in the best possible way, but he was the victim. From what I've seen on Spanish television, it's a regrettable situation and not correct, but Ruben wasn't involved in this," Balde said.
"The alleged kidnapping did not take place. It's a total lie that there was a kidnapping and torture. The gun didn't belong to Semedo even though they found it in his house."
Villarreal said on their website that they would open an investigation into the player and take any necessary action.
Semedo joined the club last year from Sporting for 14 million euros (A$22 million). He has made only three starts in LaLiga this season due to a series of injuries.