A tender for the contract to carry out feasibility studies for the project is expected to be launched shortly.
A large fire ravaged the historic building on Sunday.
The Spanish firm argues that it was disqualified from a tender for a US$800mn PPP rail project over a requirement that was not in the bidding documents.
VLI, whose main shareholder is metal and mining company Vale, reportedly seeks to buy a grain terminal.
Javier Jiménez Espriú, Mexico's future transport and communications minister, told BNamericas that corrupt firms will not be allowed to participate in public works tenders.