Fortigate - SCP

First ensure SSH is allowed on the interface you are attempting to access:

config system interface
edit <interface>
set allowaccess ping https ssh

Now enable SCP:

config system global
set admin-scp enable

To run a backup of the running configuration:

scp [email protected]<ip>:sysconfig <local-file>

In order to retrieve configuration regarding other users you must authenticate using a high privileged account.