Chapter 11 IPsec VPN for FortiOS 5.0 : IPv6 Features : IPv6 forwarding—Policies, IPS, Application Control, flow‑based antivirus, web filtering, and DLP
  
IPv6 forwarding—Policies, IPS, Application Control, flow‑based antivirus, web filtering, and DLP
FortiOS 5.0 fully supports flow-based inspection of IPv6 traffic. This includes full support for IPS, application control, virus scanning, and web filtering.
To add flow-based inspection to IPv6 traffic go to Policy > Policy > IPv6 Policy and select Create New to add an IPv6 Security Policy. Configure the policy to accept the traffic to be scanned. Select Security Profiles and select the profiles to apply to the traffic.