It is uncertain how long the facility will remain closed. Reforma said the neighbors had asked for a meeting with Bishop Ortiz and promised to block any migrants from entering their street, which dead ends at the rail yards.
Calls to the St. Juan Diego shelter went unanswered. Attempts to reach a representative from the bishops' human mobility ministry were unsuccessful.
The closure ended an escalating conflict with neighbors but leaves hundreds of undocumented Central Americans without a place to find assistance on a long leg of their northbound journeys across central Mexico.
It highlighted again the difficulties and inhospitable situations awaiting the migrants transiting Mexico, where they commonly face crimes such as robbery, rape and kidnap.
The shelter opened in 2007, but strife started with the neighbors in 2010 as the facility was unable to deal with a crushing demand of migrants, many of whom would end up sleeping in the street.
Shelter officials began limiting stays to just one night because of the demand.
Reforma reported 50 migrants had been staying at the shelter at the time the closure was announced.
Northbound migration on the trains has been slowed in recent weeks because of damage to railroad infrastructure caused by Hurricane Carlotta in Oaxaca state. Because few trains are headed north, migrants have been stranded across southern Mexico, said Father Heyman Vazquez Medina, director of a shelter in neighboring Chiapas state.
Father Vazquez estimated at least 800 migrants were stranded at his shelter but added that local parishes in the municipality of Arriaga were pitching in to help.
The railway operator, Ferrocarril del Sureste, estimates repairs will be completed by July 17, it said in a press release.
Shelter operators have said migrants from Central America still head north in large numbers, despite risks along the route from criminal gangs and crooked public officials.
Mexico's National Immigration Institute said in a July 5 statement it was offering humanitarian aid to stranded migrants in four southern states. An immigration director, however, told the news service Notimex that the migrants were ineligible to stay in Mexico and would be returned to their countries of origin.