Only nine of the 21 birds found stuffed in plastic water bottles in the luggage of a suspected wildlife smuggler survived, said a conservation group which provided updates on the case widely reported earlier this month.
The remaining birds, mostly cockatoos, are now at the Maharani Zoo in East Java.
Indonesian police made the shocking discovery on May 4 when they stopped a 37-year-old man as he alighted from a passenger ship at Port of Tanjung Perak in Surabaya, a city on the main island of Java. The man has been arrested.
Photographs showed the birds peering out of the bottles after being found by officers. The bottoms of the bottles had been cut off to squeeze the birds inside.
It was pure chance that led to the startling discovery, according to Mr Mehd Halaouate, the breeding and release centre manager at the Begawan Foundation. He visited the surviving birds at the Maharani Zoo on behalf of the World Parrot Trust.
The 21 sulphur-crested cockatoos and one eclectus parrot had already endured four days and nights at sea when they were rescued by Indonesian police. The species are found on the Kai and Aru Islands of Maluku in eastern Indonesia.
The suspected smuggler, who travelled from Ambon Island, had got off the ferry during a transit with one of the birds - a green-coloured eclectus parrot on his shoulder.
He did not know that a permit was required to transport wildlife. The police at the harbour arrested him, but did not know about the other birds.
On seeing his arrest, passengers on the ferry told the police that they heard screeching and squawking coming from two big bags on the boat. These bags contained the plastic bottles that the cockatoos were trapped in.
Mr Halaouate said in his report: "I personally felt really sick. I have been around and seen smuggling attempts conducted in many ways but never this cruel."
The cockatoos were in a shocking condition when they were cut free from their plastic prisons. Less than half survived the arduous journey.
Earlier reports said there were 24 birds found, but according to Mr Halaouate, police confiscated 21 sulphur-crested cockatoos and one eclectus parrot.
Media reports also said they were the critically endangered yellow-crested cockatoos, but Mr Halaouate found them to be the more common medium sulphur-crested cockatoo. The two look similar, and can be confused.
While the sulphur-crested cockatoos are still found in good numbers in the wild, there is intensive trapping and capture of this species for the pet trade, Mr Halaouate said. Some smuggled birds end up in Singapore for private collections.
The discovery last month is not an isolated incident, said Mr Halaouate. Several months earlier, 20 sulphur-crested cockatoos were delivered to the zoo after they were confiscated in the same harbour.
The zoo is struggling to care for all of them as these unplanned additions have stretched their budget, but the World Parrot Trust has raised some funds for the cockatoos.