An example method of propagating fault domain topology information in a distributed container orchestration system includes: receiving, at control plane software executing in a data center, the fault domain topology, which includes tags for a protection group and fault domains for remote sites in communication with the data center; deploying, by a master server of the distributed container orchestration system that executes in the data center, a node pool comprising virtual machines (VMs) executing in servers of the remote sites, the VMs being nodes of the distributed container orchestration system in which containers execute; determining, by a controller of the master server, relationships among the VMs, the servers, the protection group, and the fault domains based on state of resources maintained by the master server; and providing, by the controller, labels to the servers for associating the tags of the protection group and the fault domains to the VMs.