Even as police were searching for him, her son called her from a taxi en route to Chile.
She said she explained the seriousness of the situation to him, telling him he was wanted for murder.
"And then he became very emotional and said, 'No, Mom, that's impossible.' And then he started crying and he said, 'Oh, no, they didn't do anything to her, did they?' The only thing I said was, 'Go to the police now and turn yourself in,'" she said.
Joran van der Sloot is accused of murdering Flores exactly five years to the day that Holloway went missing in Aruba.
He is also charged with extorting $25,000 from Holloway's mother, Beth Twitty, promising to show her where the teen's body was buried in exchange for the money.
Anita van der Sloot found the timing incredible.
"I thought, 'This is a set-up. This can't happen,'" she said.
In the alleged confession, van der Sloot is quoted as saying he met Flores at a Lima casino and they were playing poker in his room when an e-mail popped up on his computer linking him to the Holloway case.
He claims Flores became upset and struck him. Enraged, van der Sloot allegedly smashed her in the nose with his elbow. Blood gushed out and she nearly fainted from the blow, the confession states. He then grabbed her by the throat and banged her head against the wall, the confession says. He finally used his shirt to smother her, according to the alleged confession.
As ABC News reported at the time of his arrest, van der Sloot appeared confused before signing some police documents. He even asked his interrogators, "This only says I understand what my rights are, correct?"
As details emerged, Anita van der Sloot has found it hard to proclaim her son's innocence, as she has in the Holloway case.
"I think a part of me still wants to believe that it's all a very bad movie. But I thought immediately of the parents of the girl," she said, referring to Flores.
In a way, she, too has lost her child, she said.
She said she won't visit her son in prison.
Her son has acknowledged he was to blame for being in a Peruvian jail, telling De Telegraaf that he should have listened to his mother and that he understood why she won't visit him in prison.
"I have caused her and many other people too much pain. If only I had listened to her," van der Sloot said.