One of the conjoined twins who were flown from Papua New Guinea to Australia in a desperate attempt to save their lives has died following an emergency surgery.

Tom and Sawong were almost two months old when they were rushed into a seven-hour surgery at Sydney Children’s Hospital on Sunday.

Tom, the most critical of the two, died, while Sawong survived the separation.

Tom has died after a seven-hour emergency surgery. (Supplied)

Medevac pilot Jurgen Ruh, who has stayed with the family, said the parents were feeling a mixture of sadness and relief.

Sawong is in critical but stable condition and under close intensive care.

He is expected to remain in Sydney for the next few months until the hole in his stomach closes.

“In the first day, he made vast improvements on his medical condition. He is getting better as fast as he can,” Ruh told 9news.com.au.

A funeral is being prepared for Tom. 

The brothers were almost two months old when they rushed into the operating room. (Supplied)

The brothers were born attached at the lower abdomen in the remote province of Morobe on October 9 and shared several critical organs, including parts of their liver, bladder and gastrointestinal tract.

Tom also had further issues, including a congenital heart defect and only one kidney. 

Ruh said it was lucky the local hospital could perform the C-section needed to deliver the babies, as only one in 200,000 conjoined twins are born alive.

The brothers were receiving treatment in Port Moresby for several weeks, but the hospital could not perform the separation surgery.

Their parents sought help from Australia, Germany and India.

The conjoined twins were flown to Sydney. (Supplied)

At the time, their father said: ”Tom and Sawong are fighters and have fought since.”

The parents were in the process of making arrangements for Germany when Tom’s health deteriorated on Thursday, and the twins were rushed to nearby Sydney. 

Specialists from the Sydney Children’s Hospitals Network had helped with the transfer.

Papua New Guinea’s Prime Minister James Marape told reporters he was assured that the Australian government would cover the medical bills.

The twins were assessed in Sydney.

Ruh said specialists believed Tom had very little chance of surviving their separation.