Prism Central VM is can’t be deleted from Nutanix web interfaces. We should use acli (acropolis CLI) to delete the VM.
Identify the cluster on which the Prism Central VM that you wish to delete has been deployed. Copy the Prism Central VM name from this cluster.
Unregister and clean up all clusters registered to Prism Central. Follow KB-4944 for the steps to unregister and clean up a cluster from Prism Central.
Check if all clusters have been unregistered from Prism Central by executing the following command from any CVM in each cluster:
ncli> multicluster get-cluster-state
The output of the above command should return [None].
Delete the Prism Central VM.
SSH to any CVM of the cluster identified in step 1 (where Prism Central is running) and execute the command below, specifying the Prism Central VM name (also from step 1), to delete the Prism Central VM:
Login to the hypervisor management software, for example vCenter or SCVMM. Then select the Prism Central VM (also from step 1) and delete the Prism Central VM.
Check if the Prism Central VM has been deleted by logging into the cluster’s Prism Element UI and browsing the VM section.
Sources: Nutanix Wiki