Native IPv6 firewalling is only supported in kernel versions 2.4+. In older 2.2- you can only filter IPv6-in-IPv4 by protocol 41.
Attention: no warranty that described rules or examples can really protect your system!
Audit your ruleset after installation, see Section 19.3 for more.
Since kernel version 2.6.20 (February 2007) IPv6 connection tracking is fully working (and does not break IPv4 NAT anymore like versions before)
Since kernel version 3.9.0 (April 2013) NAT for IPv6 is supported with ip6tables >= 1.4.18
Since kernel version 3.13 (April 2014) new framework introduced named: nftables