But criminal charges haven't been filed against him yet.
And his family is suggesting any confession might have been forced out of him, reports CBS News Correspondent Elaine Quijano
In coming days, the Dutchman is expected to be taken back to a Lima hotel room to re-enact the crime.
Van der Sloot's mother spoke to her 22-year-old son and says the confession may have been coerced.
She spoke to the family's Dutch attorney, Bert de Rooij, who told CBS News, "He said, 'I'm being interrogated in a very rude way' … and he said, 'I think they are aiming at a coerced confession." '
Van der Sloot's mother has also, Quijano notes.
On Monday, police say, van der Sloot told them he killed Flores, 21, reportedly adding he became enraged when he caught her looking up information about the Natalee Holloway case on his laptop and questioning his involvement in the.
Holloway was last seen in Aruba with the Dutchman five years ago. He was held and questioned in that case twice, was never charged, and remains the prime suspect.
In a crime scene report obtained by CBS News, authorities say Flores' body was found lying face down, in a t-shirt and panties, with a bruised face and knees. Cause of death is listed as a broken neck.
The question now is what effect, if any, van der Sloot's apparent confession will have on the Holloway case.
"Peruvian authorities," says CBS News legal analyst Trent Copeland, "may look at this and say, 'Listen, I'm not gonna send him back to Aruba, where he wasn't prosecuted to begin with, especially if we're under no affirmative obligation to do so." '
Separately, the New York Post reports new details on extortion counts van der Sloot faces in the United States.
Citing an unnamed source, the newspaper says the FBI paid van der Sloot $25,000 as part of a sting operation, and he used the money to pay for his trip to Peru.
"Van der Sloot tried to shake down Holloway's mother," says the Post, by offering information about Natalee's disappearance.
On "The Early Show" Wednesday, former prosecutor Beth Karas, now a correspondent for truTV's "In Session," said developments in the case in Peru could well impact those in Aruba and the U.S.: