The US$18mn project involves adding stretches to the access road network of Esmeraldas city in Ecuador.
According to the ministry, the funds will be used for works under various contracts for building, repairing and maintaining roads and highways.
Using highway tolls is one option on the table, according to a report.
The country's new president will take over in January.
President Martin Vizcarra edged closer to securing approval for his anti-corruption drive after the opposition-controlled congress gave his government a vote of confidence.
Lawmakers approved a bill that establishes the procedure to decide the compensation to be paid to landowners.
The special economic zone is one of seven the Mexican federal government is working to develop.