Ali Khorram Heydarkhani, 40, was deported from Indonesia and arrested upon arrival at Sydney. He later appeared in a Sydney court to have the charges read out and was denied bail.
The trial will take place in Perth, Australia, next month.
The trial will be high profile because of the tragic nature of the shipwreck that involved an unseaworthy vessel with nearly 100 asylum seekers being smashed against a rocky coastline in rough seas.
Would-be rescuers watched on shore as people, including women and children, yelled for help and attempted to swim to shore. Many of the asylum seekers' attempts to save themselves were televised live.
Up to 50 asylum seekers drowned, including at least one baby. Coast guard vessels rescued 42 survivors, mostly Iranian, Iraqi and Kurdish asylum seekers, and recovered 30 bodies from the sea. But up to 20 people remain unaccounted for.
Indonesian police arrested Heydarkhani in January and deported him this week after his visa expired, Home Affairs Minister Brendan O'Connor said.
"Those people who seek to lure, in some cases people who are desperate, into unseaworthy vessels where people's lives are at risk, where people perish, will be punished," O'Connor said.
Like many asylum seekers, the shipwreck passengers were on their way to Australia by way of Indonesia, after paying notorious people smugglers thousands of dollars for passage on the overcrowded boat.
O'Connor said it was "the right decision" to conclude a refugee swap agreement with Malaysia in an attempt to thwart the people smugglers. ''We do not want to see any more tragedies. We do not want to see men, women and children perish at sea,'' O'Connor said.
Over the next four years, Australia will send around 800 boat people to Malaysia as soon as they arrive in Australian waters and are picked up by Australia's coast guard and navy.
For every person transferred to Malaysia, Australia will take five refugees from Malaysia on condition that they haven't been boat people. This means an additional 4,000 refugees arriving in Australia, the government estimated.
The deal is part of a "regional cooperation framework" that Canberra said is aimed at putting out of business notorious people smugglers operating across Asia, as well as stemming the tide of boat people heading for Australia.
Australia's Department of Immigration said 134 boats carrying 6,535 people arrived last year. So far this year, 16 boats carrying around 920 people have been intercepted by Australian authorities.
A big issue for successive Australian governments is ensuring enough detention centers to house them while their asylum status is investigated.
The detention center on Christmas Island -- around 1,600 miles from Australia's west coast but less than 200 miles from Indonesia -- is at its capacity of around 1,700 people.
Australia also is in discussions with Papua New Guinea about reopening a former detention center on PNG's remote Manus Island.