The anti-virus guru was detained at a hotel in an upscale Guatemala City neighborhood with the help of Interpol agents and taken to an old, three-story building used to house migrants who enter the country illegally, said Interior Minister Mauricio Lopez Bonilla.
"He will be in danger if he is returned to Belize, where he has denounced authorities," said his lawyer in Guatemala, Telesforo Guerra. "His life is in danger."
Guerra said he would ask that a judge look at McAfee's case as soon as possible. "From the moment he asked for asylum he has to have the protection of the Guatemalan government."
McAfee, founder of the McAfee software security company, had formally requested asylum in Guatemala after fleeing Belize, where he has lived for the past three years. McAfee is wanted for questioning in the murder of his neighbor on Ambergris Caye in Belize.
Greogry Viant Faull was found fatally shot in November on the small island off the coast of Belize. Faull was McAfee's neighbor. The two had confrontations about McAfee's dogs.
McAfee claims Belizean authorities are persecuting him because he hasn't donated to local politicians. He went into hiding after Faull's murder, but has been in contact with reporters and has been writing on his blog.
Belizean police say there is no warrant for McAfee's arrest. McAfee does not have travel restrictions, so it was unclear why he would need formal protection in Guatemala.
McAfee has been described as an eccentric practical joker. He sold his antivirus software company in the 1990s. He moved to Belize about three years ago to lower his taxes.
Neighbors in Belize have complained about his aggressive dogs, illegal weapons and drug activity. His dogs were fatally poisoned shortly before Faull's murder.
He had earlier said he didn't plan to leave Belize but ultimately did because he thought "Sam" was in danger, referring to the young woman who has accompanied him since he went into hiding.
"Yes, we are presenting this, and I want it to be clear, because of the persecution, not because of the murder," he told the Associated Press.
Faull, 52, was found dead with a gunshot wound to the head. His body was found inside his home near San Pedro, a town on the island of Ambergris Caye in Belize. His computer and phone were missing. No signs of forced entry were found. Faull was an American citizen. Other neighbors were questioned about the murder.
McAfee Inc. was sold to Intel in 2010 for $7 billion.
The Associated Press contributed to this report.