The haul, estimated to have a street value of A$1bn (£600m; $800m), was uncovered when police raided a dock in Western Australia, authorities said.
Police have charged the men, each of whom faces a maximum penalty of life in prison.
Crystal methamphetamine, also known as ice, has been described as the most damaging illicit drug in Australia.
The 1.2-tonne (2,650lb) bust was larger than the previous record seizure, made in Melbourne in April.
