The Ministry of Public Administration (SFP) is currently investigating a number of environmental irregularities related to the construction of Section 5 South of the Maya Train project. This section, which will stretch from Playa del Carmen to Tulum, is overseen by companies ICA, Mota-Engil Latin America, and Azvindi Ferroviario.

According to an audit report, as of December 2023, the project has shown "insufficient evidence of actions resulting from the authorization of Regional Environmental Impact". In addition, there are "deficiencies in the implementation of flora and fauna management programs, and conservation of soils and reforestation".

The SFP has also documented other irregularities, such as "deficiencies in the implementation of the integral water management program for monitoring the quality of surface and groundwater”. Furthermore, there’s an “absence of established wildlife crossings in subsection C of Section 5 South, of the Maya Train project.”

One audit highlighted a "potential impact of soil damage due to generation, handling, storage and inappropriate disposal of solid, liquid, special handling and hazardous waste". The audit also revealed that during inspections carried out between August 21 and 25, 2023, "absorbent mats are not used for protection against possible spills in most of the machinery on the site".

Attempts to reach Fonatur Maya Train for comment were unsuccessful. The project is currently undergoing a transition to the Secretariat of National Defense (Sedena), as outlined in a decree published on March 1.

The SFP also found that in the three subsections of the South Section of the Maya Train (A, B and C) "drainage works allowing adequate hydrological flow were not identified". Moreover, "it was not reported nor was there evidence on-site that showed the construction or delimitation for the establishment of all the planned hydrological wells".

On February 16, a federal judge in Yucatán ordered a halt to the works in the section due to impacts on the subsoil. The federal government was also ordered to deliver the studies.