Interior Minister Mauricio Lopez Bonilla said McAfee was detained by police at a hotel in an upscale Guatemala City neighborhood with the help of Interpol agents. He offered no other details.
Earlier Wednesday, McAfee said he had formally requested asylum in Guatemala, claiming he is the victim of persecution in neighboring Belize where officials have said he is a person of interest in the killing of a fellow ex-pat.
McAfee was taken late Wednesday to an old, three-story building used to house migrants who enter Guatemala illegally.
The 67-year-old went on the run from Belize last month after officials tried to question him about the fatal shooting of a neighbor. McAfee had engaged in a series of clashes with neighbors and authorities over allegations he kept aggressive dogs, illegal weapons and drug paraphernalia in his beachfront home on a Belize island. McAfee has denied any wrongdoing and said he was being persecuted for refusing to donate to local politicians.
He dropped out of sight for weeks after police said they were seeking him, although he grabbed global attention by recounting his life on the run through a blog and regular phone calls with reporters. He crossed into Guatemala this week and told The Associated Press that he formally applied for asylum Wednesday.
"Yes, we are presenting this, and I want it to be clear, because of the persecution, not because of the murder," he told the AP.
Belizean officials have denied persecuting McAfee, and the country's prime minister has said he suspects McAfee is mentally unstable.
Police in Belize say there is no warrant for McAfee's arrest. Since there are no restrictions on his travels, it's unclear why he would need any special status in order to stay in Guatemala.
McAfee is wanted for questioning in connection with the killing of Gregory Viant Faull, who was shot to death in early November on the Belize island where both men lived.
Faull's home was a couple of houses down from the compound where McAfee kept several noisy dogs and armed guards and entertained a steady stream of young women brought in from the mainland. McAfee acknowledges that his dogs were bothersome and that Faull had complained about them, but denies killing Faull. Several of the dogs were poisoned shortly before Faull's killing.
The Faull family has said through a representative that the murder of their loved one on Ambergris Caye has gotten lost in the media frenzy provoked by McAfee's manipulation of the press through phone calls, emails and blog posts detailing his life on the lam.
For two weeks, McAfee refused to turn himself in to authorities in Belize and claimed to be hiding in plain sight, wearing disguises and watching as police raided his house. It was unclear, however, how much of what McAfee - a confessed practical joker - said and wrote was true.
McAfee hasn't provided details on how he crossed from Belize into Guatemala.
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.
McAfee, the creator of the McAfee antivirus program, has led an eccentric life since he sold his stake in the anti-virus software company that is named after him in the early 1990s and moved to Belize about three years ago to lower his taxes.
He told The New York Times in 2009 that he had lost all but $4 million of his $100 million fortune in the U.S. financial crisis. However, a story on the Gizmodo website quoted him as calling that claim "not very accurate at all." He has dabbled in yoga, ultra-light aircraft and producing herbal medications.
(Copyright 2012 by The Associated Press. All Rights Reserved.)