The flight carrying Alex Shorey, 24, landed in Brisbane on Wednesday night after stopping in Darwin and Mt Isa.
He was transferred to the clinical toxicology unit at the Princess Alexandra Hospital, where he was in stable condition on Thursday.
Mr Shorey was on a university exchange in Taiwan's capital Taipei when he fell seriously ill several weeks ago.
The university student from the Queensland city of Toowoomba might have inadvertently ingested food contaminated with superwarfarin, according to an online fundraiser set up by his aunt Elizabeth Shorey-Kitson.
Superwarfarins are a potent type of anticoagulant commonly used in rat poisons.
Ms Shorey-Kitson said he suffered haemorrhaging and a life-threatening anaphylactic reaction to treatment in hospital and the family wanted him back in Australia for further care.
A medical charter flight was secured after raising more than $200,000 through donations.
Ms Shorey-Kitson said her nephew was still critically unwell and required oxygen and IV medication.
The specialised medical charter flew at a lower altitude to ensure there were no further medical complications and to support his respiratory system, she said in a statement on the site.
"As Alex's condition will now require long-term rehabilitation, he needs to get home to Australia to be around his family," Ms Shorey-Kitson said.
She again thanked people who sent donations and messages of support, and the Taiwan health staff who treated him.
"We are extremely grateful to Alex's medical team for their expertise and the care they've shown in treating him. We thank you all so much for everything you've done, we will be forever thankful."
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