It's alleged the couple, who arrived at Sydney Airport on September 27, were carrying a total of 1.3kg of heroin in 173 pellets in their stomachs.
The 36-year-old man sparked a quarantine and medical bird flu emergency after falling ill on his Vietnam Airlines flight.
Police say one or more of the pellets burst inside him, resulting in a massive overdose.
He was later cleared of bird flu but allegedly had 80 pellets containing 457g of heroin surgically removed from his stomach, the Australian Federal Police (AFP) said today.
His fiancée, also 36, who accompanied the man to St George Hospital soon after their arrival in Sydney, later passed 93 pellets containing 912g of heroin, the AFP alleges.
The couple, both Australian nationals from Greystanes in Sydney's west, have been charged with drug trafficking.
The man, who was charged on Friday during a bedside court hearing in hospital, was due to appear in Kogarah Local Court today.
AFP officer Bruce Hill said it is thought one or more of the pellets burst inside the man, resulting in a massive overdose.
"Immediate medical attention and surgery to remove the pellets were the only things that prevented this man from losing his life," federal agent Hill said.