This bug/flaw is by design. The Minecraft launcher disables IPv6 (by setting "java.net.preferIPv4Stack" to true). The only workarounds for this are to use a 3rd party launcher or to modify the official one.

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This appears to be a problem with the Minecraft launcher, rather than the minecraft.jar file itself. The launcher sets the "java.net.preferIPv4Stack" property to true and the "java.net.preferIPv6Addresses" to false, prohibiting the use of IPv6 on systems configured as described. Adjusting these two properties should fix the problem.

If Minecraft is started with a 3rd party launcher (such as MultiMC) that doesn't modify these properties as above, it operates correctly.

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Since the new multiplayer interface, Minecraft no longer works for me when using IPv6.

My home network is configured using IPv6, while Internet is only IPv4. Each system has a statically assigned IPv6 address in the unique unicast range fc00::/7. Hostnames have been added for these addresses to each system's hosts file.

What I expected to happen was...:
I should be able to connect to local IPv6 servers.

What actually happened was...:
IPv6 hostnames fail to resolve. IPv4 hostnames in the hosts file do resolve.
A fix in 1.4.5 allows IPv6 addresses to be used, but they fail to connect with the error "Protocol family unavailable".

Steps to Reproduce:
1. Add a server or direct connect using a hostname that resolves only to IPv6 or using an IPv6 address ([::1] or [fc00::1]).
2. Try to connect.

This may require limiting Internet to only use IPv4. I don't have access to IPv6 Internet, or I'd try and see if that works correctly.

If I revert to Minecraft 1.2.5, I can connect to any local IPv6 servers by hostname or IPv6 address without failure.

All other applications I have that support IPv6 work with my network setup.