Runner was not on board team plane despite assurances he would not be punished for taking a stand over political repression in his country.
An AFP journalist at the airport in Addis Ababa said Lilesa was not on board the plane that landed on Monday night carrying Ethiopia’s Olympics team.
Ethiopian sports officials congratulated team members but made no mention of Lilesa’s silver medal achievement – one of only eight medals won by Ethiopia – and refused to answer any questions about the athlete.
On Sunday, Lilesa, who came second to Kenyan favourite Eliud Kipchoge in Rio, crossed his arms as he finished the marathon in a symbolic protest against the repressive Ethiopian regime.
The 26-year-old repeated the gesture during the race’s medal ceremony, saying he was afraid to go back to his homeland.
Lilesa’s agent Federico Rosa had earlier told AFP that the runner would not be returning home after staging his protest, despite Ethiopian government assurances he would not face any issued if he went back.
“He doesn’t want to go to Ethiopia, he wants to go to another country,” the runner’s agent, Federico Rosa, told the New York Times. “I don’t know even when he decided to do this,” he added.
“I don’t think that there is any way that he will [go back to Ethiopia],” Rosa told AFP earlier on Monday. “There are many people who say that it would not be good for him to go back.”
Rosa, who is based in Italy and has been the athlete’s agent for three years, said he did not know exactly what his client was planning to do next, having stayed on in Rio at the end of the games.
“I cannot say for sure because I have not spoken to him since just after the race, when we had a very short conversation,” added.
The Internet has rallied behind Lilesa, with a crowdfunding campaign raising more than $100,000 for him.
“You don’t do something like this for money,” Rosa said. “He did this to defend his country.”
Reports have suggested that the runner may seek political asylum in the United States.