The vandalism was discovered by a worker who reported the incident to his superiors before removing the graffiti.
This is the second such incident after two trains at the depot in Thu Duc City were sprayed with graffiti last June.
None of the culprits have been found so far.
HCMC Management Authority for Urban Railways said security is usually tight at the depot and the construction contractor is responsible for it.
MAUR is working with various agencies to investigate, he said.
The Long Binh Depot spreads over 20 hectares and will serve as the control center and train maintenance yard.
The VND43.7-trillion (US$1.89 billion) metro, after several delays, is now 95 percent complete and expected to finally be finished this year.