Thai authorities had gifted the 29-year-old Muthu Raja, also known back in his birthplace as Sak Surin, to Sri Lanka in 2001.
But they demanded it back last year after allegations it was tortured and neglected while housed at a Buddhist temple in the island nation’s south.
The 4,000-kilogram (8,800-pound) mammal flew out from Colombo airport on Sunday morning on a one-way commercial flight for a repatriation that Thai officials said had cost $700,000.
The Ilyushin IL-76 cargo plane carrying Muthu Raja took off around 7:40 am (0210 GMT), the airport manager said.
After touching down in Chiang Mai the elephant will be quarantined at a nearby nature reserve.
It was taken from its temporary home at a zoo in Colombo before dawn in a special steel cage the size of a shipping container.
Four Thai handlers alongside a Sri Lankan keeper are accompanying the elephant on the flight and two CCTV cameras will monitor its health in transit.
The chief veterinarian at the Dehiwala Zoo, Madusha Perera, told AFP that Muthu Raja was in pain and covered in abscesses when he was rescued from his previous abode last year.
Animal welfare groups said the elephant had been forced to work with a logging crew and its wounds — some allegedly inflicted by its handler — had been neglected.
The elephant will undergo hydrotherapy to treat a remaining injury on its front left leg when it returns to Thailand, Perera said.
Elephants are considered sacred in Sri Lanka and they are protected by law.
The organization Rally for Animal Rights and Environment (RARE), which led a campaign to rescue Muthu Raja from the temple, has expressed its unhappiness over the animal’s departure.
RARE organized a Buddhist blessing for the elephant on Friday ahead of the journey and the group is now petitioning the authorities to prosecute those it says are responsible for neglecting the animal.
A nationalist group staged a demonstration outside the Thai embassy in Colombo on Thursday demanding the animal remain in Sri Lanka for another six months.
“We did not know about the plight of the elephant,” the group’s leader Dan Priyasad told AFP.
“We can nurse it back to health in six months and if we fail, they can take the animal back.”
Wildlife minister Pavithra Wanniarachchi said Thailand had been “adamant” in its demands for the elephant’s return.
Prime Minister Dinesh Gunawardena told parliament in June that he had personally conveyed Sri Lanka’s regrets to the Thai king over the elephant’s condition.
Thai environment minister Varawut Silpa-archa would not be drawn last month on whether Muthu Raja had been mistreated but noted that the Thai government had stopped sending elephants abroad.
Bangkok’s diplomatic missions were now checking the condition of those already sent overseas, he said.
