The parents of a little boy who suffers from a rare genetic condition say his life would be at risk if he is deported from Australia, after his application for permanent residency was rejected over the cost of his ongoing care.

Key points: Shaffan Ghulam has a disorder that affects the strength of his bones and breathing

Shaffan Ghulam has a disorder that affects the strength of his bones and breathing His parents say the low pressure environment of a plane could kill him

His parents say the low pressure environment of a plane could kill him They have appealed to the Immigration Minister to intervene on his behalf

Shaffan Muhammad Ghulam has a rare genetic disorder called chondrodysplasia punctata that affects the development of his bones.

He suffered a partial break on his spine when he was six months old, leaving him paralysed.

He is getting better at breathing on his own, but he still relies on a ventilator and needs round-the-clock medical care.

Now he is facing deportation to his parents' home country of Pakistan, but his family say they have medical advice that he is at significant risk of respiratory decompensation in the low-pressure environment of an airplane, which could kill him.

Shaffan Ghulam requires a ventilator to breathe most of the time. ( ABC News: Hugh Sando )

Shaffan was born in Australia in 2014, five years after his father came here to study.

His father, Qasim Butt, completed his masters in accountancy and remained in Australia on a graduate visa that allowed him to work.

When that ran out in 2016, he and his wife applied for permanent residency for themselves, Shaffan, and their two-year-old daughter.

But after completing a medical assessment they were told they were not eligible because their son's ongoing medical care needs would "likely result in a significant cost to the Australian community".

"That is very devastating we are rejected on the basis of the cost," Mr Butt said.

A broken spine at six months old left Shaffan paralysed from the neck down and his breathing compromised. ( ABC News: Hugh Sando )

"We understand that whatever decision we got, that is according to the law, which is acceptable, but [at] the same time I think that is not fair, that the department is not considering his current situation."

The family say while the community in Perth have rallied around them, they have been placed under enormous pressure after their appeal of the department's decision was rejected.

"They understand us, they understand my son's condition and I am sure that they consider that as a human being Shaffan's life is more important than a medical expense," he said.

Mr Butt said Shaffan will not receive the help he needs in Pakistan.

Mr Butt uses a specially-designed chair to take Shaffan on a nightly walk to the park. ( ABC News: Hugh Sando )

"We all know that the health care system that Shaffan is getting in Australia is the best," he said.

"Shaffan is five years old and he is improving.

"We are so happy that Shaffan is in good hands, so I think [the] Minister needs to consider on compassionate grounds, this is the last chance for us.

"This is the last hope for Shaffan as well.

"We don't want to be putting our child at risk."

Appeals of deportation decisions in Australia are reviewed by the Administrative Appeals Tribunal.

Under the Migration Act, if an appeal is not successful an individual can ask the Minister to personally intervene on their behalf, and prevent their deportation.

The Butt family have submitted a formal application to the Minister on compassionate grounds.

A spokeswoman for the Department of Home Affairs said they could not comment on individual cases.

But she said individuals could apply for ministerial intervention and could stay in the country until their case was reviewed.