McAfee, who had been in hiding for three weeks, crossed into Guatemala with his girlfriend, Samantha, to evade authorities in Belize who wanted to question him as "a person of interest" about the killing of fellow American Gregory Faull.
"He entered the country illegally and we are going to seek his expulsion for this crime," Interior Minister Mauricio Lopez Bonilla said.
Guatemala government spokesman Francisco Cuevas said McAfee would be expelled to Belize and he expected the process to be completed by early Thursday morning.
There is no international arrest warrant for McAfee. Police in Belize say he is a person of interest in their murder investigation and is not a prime suspect.
McAfee was taken to a residence belonging to the immigration department guarded by a small group of police.
On Tuesday, McAfee said he would seek political asylum in Guatemala, which has been embroiled in a long-running territorial dispute with Belize. There is no extradition treaty between the two countries, and there is no international arrest warrant out for McAfee.
McAfee says he fears Belizean authorities would kill him if he returned there for questioning. Belize's prime minister has denied the claim, calling the 67-year-old software entrepreneur paranoid and "bonkers."
McAfee has been living in the tiny Central American nation for about four years.
He was one of Silicon Valley's first entrepreneurs to build an Internet fortune. The former Lockheed systems consultant started McAfee Associates in the late 1980s.
McAfee has no relationship now with the company, which has been sold to Intel Corp. (Additional reporting by Sofia Menchu and Lomi Kriel; Writing by Gabriel Stargardter; Editing by Simon Gardner and Philip Barbara)