The European bank approved a US$104mn loan to renovate the rolling stock of line D, among other improvements.
The group now reportedly comprises investors holding 50% of the US$6bn in bonds that were originally issued in two separate offers by the Mexico City Airport Trust (MEXCAT) on behalf of GACM, the state holding tasked with developing the mega project.
The first phase will focus on the rehabilitation of existing rail tracks.
The northeast port is used mainly for exports of soybeans to Asia.
CCR, operator of the route between Brazil's two largest cities, said it will appeal the order.
The multilateral lender is urging the region's governments to enact a comprehensive climate-resilience strategy that includes stronger insurance and infrastructure frameworks ahead of hurricanes fuelled by global warming.