Judge Juan Buendia issued the order before dawn Friday, instructing penal authorities to place the Dutchman in a penitentiary pending trial.
Van der Sloot is reportedly trying to cop a plea deal that, reports say, could result in a nine-year prison sentence.
Investigators say Flores, a 21-year-old business student, had a broken neck when her body was found.
Van der Sloot, 22, remains the lone suspect in the 2005 disappearance in Aruba of Alabama teen Natalee Holloway.
He is also said to be offering to tell authorities in Aruba - and only in Aruba -- where Holloway is buried. The Alabama teen disappeared on the island five years ago; Van der Sloot was held on two separate occasions during the investigation of her disappearance, but never charged.
No one is sure if he really knows Holloway's body's whereabouts, or how his reported offer plays into the possible plea deal in the Flores death, reports CBS News Correspondent Elaine Quijano.
The deal, she says, would consist of Van der Sloot pleading guilty to a lesser charge of emotional violence, as opposed to murder, which carries a possible 35-year term.
Does Van der Sloot Know Where Natalee Is?
Affidavit: Van der Sloot Lied about Natalee
Moment Van Der Sloot Met Flores Caught on Tape
Van der Sloot Called "Homicidal Maniac"
Flores Kin Was "Freaking Out" over van der Sloot
Van der Sloot Lawyer: Inconsistencies Already
Peruvian Police General told reporters that, "According to the preliminary diagnostics, (the events in the hotel room fit) into the picture of a violent psychopath who has no control over his emotions."
Peruvian officials are confident of a conviction in the Flores case because, they say, he confessed, and due to surveillance video showing Van der Sloot and Flores in a casino together and entering his hotel room. It also shows him leaving the room - alone.
A conviction is likely in Peru, observes former prosecutor Beth Karas, who's now a correspondent for truTV's "In Session." Says Karas, "He faces a maximum of 35 years. (There) could be leniency because he confessed. However, there are many who feel that he won't get leniency because of the particular circumstances here."
In the United States, Van der Sloot faces extortion and wire fraud charges. An FBI affidavit unsealed Thursday reveals how, the agency says, Van der Sloot negotiated the terms of an extortion deal between himself and Natalee Holloway's mother, a deal that would have netted him $250,000 in exchange for his telling where to find Natalee's body. The document says Van der Sloot claimed he had "thrown Natalee to the ground," and that, "She hit her head on a rock and died as a result of the impact."
As part of the prospective plea pact, Quijano points out, Van der Sloot's Peruvian attorney wants the confession dismissed since, the lawyer asserts, it was coerced.