Chapter 1 What’s New for FortiOS 5.2.1 : System Features : Netflow v9.0 : Using Netflow with VDOMs
  
Using Netflow with VDOMs
For VDOM environments, excluding the management VDOM, Netflow must be configured using the following CLI commands:
config system vdom-netflow
set vdom-netflow enable
set collector-ip <address>
set collector-port <port>
set source-ip <address>
end