"I've received threats, many threatening e-mails. I'm an older person. This isn't for me," Maximo Altez, 54, told The Associated Press.
He would not describe the threats in a brief telephone conversation, saying only that he would stop representing the young Dutchman when members of Van der Sloot's family arrive in Peru in the next few days.
Police say Van der Sloot confessed last week to killing a 21-year-old Lima student, Stephany Flores, on May 30 in his hotel room after the two met playing poker at a casino.
Van der Sloot, 22, also remains the lone suspect in the disappearance exactly five years earlier in Aruba of U.S. teen Natalee Holloway. He was twice arrested and freed in that case for lack of evidence.
It was not known who will replace Altez. Dutch officials said before Van der Sloot was charged last week that his mother, a schoolteacher in Aruba, might have to borrow money in order to afford defense counsel. She has refused to talk to reporters.
A Peruvian judge on Friday ordered Van der Sloot jailed pending trial.
A different judge, Carlos Morales, will preside over the case, said court spokesman Luis Gallardo. It is not known when the trial will begin.
Prosecutors say Van der Sloot acted with "ferocity and great cruelty" in allegedly killing Flores. According to a transcript of the confession police say he made, Van der Sloot elbowed the young woman in the nose, strangled her with both hands, threw her to the floor, took off his bloodied shirt and asphyxiated her.
If convicted, he faces from 15 to 35 years in prison.
Van der Sloot is being held in a segregated block of the maximum-security Castro Castro prison in eastern Lima. He asked to be separated from the main prison population out of fear for his life.
The Dutchman has his own 2-by-3.5-meter (6.6-by-11.5-foot) cell, which is adjacent to that of a reputed Colombian hit man, a spokesman for the National Penal Institute told the AP, speaking on condition of anonymity for security reasons.
Both share the television set in the Colombian inmate's cell, the spokesman said.