But opposition from hotel owners led him to change his route by cutting a 68-mile (110 kilometer) strip through the jungle between the resorts of Cancun and Tulum.
This faces opposition from environmentalists who say the train will crush or contaminate the network of caves and sinkhole lakes around the resorts of Tulum and Playa del Carmen.
And engineers feared the fragile, cave-carved limestone floor would collapse under the weight of the high-speed train. But the president now says two-thirds of the line will not touch the ground.
Instead, it will be raised on thousands of 80-foot (25-meter) piles driven into the stony ground, supporting pre-engineered elevated sections eight feet (2.5 meters) above the ground.
“It will have a minimal effect, because where they sink the pilots is where there is nothing,” said López Obrador.
Activists dismissed the idea that engineers could avoid caves when pouring support columns, or that the train will have no impact, noting that millions of trees have already been clearcut for the project.
“They don’t have the technical ability to sink the columns where there are no caves, because they (the caves) are everywhere,” said Jose ‘Pepe’ Urbina, a diver who explored the caverns during decades.
He said the construction was already contaminating the normally crystal-clear water that flows through cave systems in Yucatan, which has no surface rivers and relies heavily on groundwater.
“It’s stupid to build a train on this ground, to build a train in the middle of the jungle, to build a train that pollutes the water,” Urbina said.
The latest change has also raised doubts about whether such a lofty runway – which López Obrador says will include a 260ft (80m) suspension bridge over a particularly extensive cavern – can be completed as the President promised it within a year.
The 950-mile (1,500-kilometer) Maya Train Line is meant to run a rough loop around the Yucatan Peninsula, connecting resort towns and archaeological sites.
Some of North America’s oldest human remains have been discovered in the sinkhole caves called “cenotes” on the country’s Caribbean coast, which were often dry and frequented by humans 13,000 years ago.