It was not immediately clear who ordered Besigye to be stopped from travelling on the Kenya Airways flight and why the action was taken. No comment was available from the airline or government officials.
Besigye flew to Nairobi two weeks ago after sustaining wounds when Ugandan police dragged him from a vehicle and drenched him in pepper spray to prevent him from taking part in a protest over rising food and fuel prices.
“They have imposed exile on Kizza Besigye. The flight has left without him. Both he and his wife are still in Nairobi,” said Anne Mugisha, deputy foreign secretary of Besigye’s Forum for Democratic Change.
Ugandan President Yoweri Museveni is due to be sworn in for a fourth term on Thursday after winning an election in February in which Besigye was his closest opponent. Reuters