The player, who spoke on condition of anonymity, told Radio France Internationale Monday 17 players and the team doctor were in hiding in Kampala, where the team was to compete in the Cecafa Cup tournament for central and east African national teams.
"Everybody has to stay in secure places because the Eritrean government is searching for us. The Eritrean embassy in Uganda is trying to find us," the team member said.
He said he defected because he objected to his country's human rights record, its compulsory military training and President Isaias Afeworki, who he described as "the main problem."
The Eritrean team has a history of defections, Radio France Internationale said.
Four players sought asylum in Kenya after a 2006 match in Nairobi, up to 12 members of the team remained in Tanzania after a 2008 tournament and six stayed in Angola after a 2008 match.