Guatemalan authorities on Thursday said that McAfee's request for asylum had been denied, but did not explain why.
Shortly after the decision was announced, McAfee issued a plea on his blog for the public to petition Guatemalan President Otto Perez Molina to let him stay.
"Please email the President of Guatemala and beg him to allow the court system to proceed, to determine my status in Guatemala, and please support the political asylum that I am asking for," the post read.
McAfee's legal team said that they would appeal the denial to the country's constitutional court, a process that could give McAfee at least another 48 hours in Guatemala.
McAfee also began complaining of chest pain, prompting authorities to move him from the immigration centre where he had been held to a police hospital.
The computer anti-virus expert was arrested for illegally entering the country, ending a bizarre journey as a self-styled fugitive with an active blog and constant contact with the media.
McAfee told The Associated Press on Thursday morning that he had suffered chest pain in the night, but had refused hospital treatment.
"I don't like western medicine," he said.
"If the people around me are kind and compassionate, that's all that matters in life. The people of Guatemala are very kind people, so I have no complaints."
Belizean police spokesman Raphael Martinez said that officials expect McAfee to be flown back to the capital.
Police hope to question him about the fatal shooting of Gregory Viant Faull, who was shot dead in early November on the Belize island where both men lived.
There is no warrant for McAfee's arrest.
McAfee said that he had formally requested asylum in Guatemala because he feared for his safety as he has sensitive information about official corruption and he doesn't want to fund local politicians.
Since refusing to turn himself in to authorities in Belize, the 67-year-old had been in hiding, blogging his movements and calling reporters, until reappearing in Guatemala to claim asylum. He has not revealed how he crossed the border into Guatemala.
Telesforo Guerra, who is McAfee's lawyer and uncle to McAfee's girlfriend, warned on Wednesday night that McAfee's life would be in danger if he returned to Belize.
"He will be in danger if he is returned to Belize, where he has denounced authorities," Guerra said.
"From the moment he asked for asylum, he has to have the protection of the Guatemalan government."
Police in Belize deny that they are persecuting McAfee, and the country's Prime Minister has even questioned McAfee's mental state.
The creator of the McAfee anti-virus program has led an eccentric life since he sold his stake in the software company in the early 1990s and moved to Belize to lower his taxes.