The room was reportedly trashed and covered in blood, indicating a struggle had taken place.
"I know that my daughter was stabbed and that there must have been a struggle. I imagine the autopsy... that it will tell or determine more," said the victim's father, Ricardo Flores, a prominent Peruvian businessman and race car driver.
Officials believe Flores was killed exactly five years after Holloway's May 30, 2005, disappearance.
Flores' body arrived at a church in Lima Wednesday night for a wake. The victim's family said van der Sloot was the last person to see the woman alive.
"This is not the first murder this man has committed. In 2005 he did the same and because he was a minor then, and the body was not found, he walked free," Flores' father said. He also added that police found pills similar to date rape drugs located inside his daughter's car.
A hotel employee said she saw Flores and van der Sloot enter van der Sloot's room at about 5 a.m. He was then seen departing alone about four hours later.
"We have an interview with a worker at the hotel who says she saw this foreigner with the victim enter his room," Peruvian police chief Gen. Cesar Guardia told reporters Wednesday.
Police said van der Sloot fled Peru, passing through customs into Chile on a bus, and may be on his way to Argentina. Authorities in Chile confirmed that van der Sloot entered the country on May 31 and there is no record of him leaving. Police say they're searching for van der Sloot in hotels and homes in northern Chile.
An international arrest warrant was issued for the Dutch citizen.
Van der Sloot reportedly entered Peru on May 14 to participate in a poker tournament at the hotel. Authorities said he met Flores at the Atlantic City Casino on Saturday night. Surveillance cameras caught the pair leaving the casino together.
An attorney for van der Sloot in New York City, Joe Tacopina, said he did not know his client's whereabouts and has not been in touch with him since the Peru allegations emerged.
"I want that this pain that we feel at this moment, that no other parent know this pain and that this man stop killing," said Ricardo Flores. "This crime cannot go without punishment like the crime in Aruba."
Holloway similarly disappeared in 2005. The 18-year-old from Mountain Brook, Alabama, vanished while on vacation in Aruba and was last seen leaving a bar with van der Sloot on the final night of the high school graduation trip.
Van der Sloot, the son of a Dutch diplomat, was twice arrested in the case, but released without charges due to lack of evidence.
Holloway's body has never been found and van der Sloot remains the main suspect in the case, said Ann Angela, spokeswoman for the Aruba prosecutor's office.
"What's happening now is incredible," she said. "At this moment we don't have anything to do with it, but we are following the case with great interest and if Peruvian authorities would need us, we are here."
In 2008, a Dutch television crime reporter captured hidden-camera footage of van der Sloot saying he was with Holloway when she collapsed on a beach, drunk.
He said he believed she was dead and asked a friend to dump her body in the Caribbean Sea.
Judges subsequently refused to arrest van der Sloot on the basis of the tape.
Wednesday night, Natalee Holloway's mother is not commenting on these new developments Peru.
The Associated Press contributed to this report.
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