The plot spurred Australia's intelligence agency to raise the aviation threat level to "probable," prompting tighter airport security measures, before the risk was downgraded to "possible" on Thursday.
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Both men have been charged with two counts each of "acts done in preparation for, or planning, a terrorist act," the Australian Federal Police said in a statement.
Police did not release details of the plot, but will hold a news conference on Friday.
The target appeared to have been a commercial flight from Sydney to the Persian Gulf, a U.S. official familiar with the arrests has previously told Reuters.
The plot may have involved a bomb or poisonous gas, domestic media have said.
Police had earlier released one of the four arrested men, but the other remains in detention without charge, under special counter-terror laws.