The Perth Royal Flying Doctor Service flew the two women to the Royal Perth Hospital yesterday.
"We brought the most serious two patients back," Dr David McIlroy told ABC Radio.
"One lady with abdominal injuries, one lady with lung injuries probably from inhaling sea water and a bit of diesel."
He said many of the remaining injured people were treated by medical services on Christmas Island.
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At least 28 people, including children, died when their wooden vessel foundered in treacherous conditions near Flying Fish Cove on Wednesday morning.
There are 44 confirmed survivors. Eleven of the survivors are children.
Immigration Minister Chris Bowen says it is still not clear how many people were on the boat. "People who have survived say there were between 70 and 100," he told Melbourne MTR.
