A Queensland woman and her son are at risk of being deported back to the Philippines because of the 10-year-old boy's autism diagnosis.

Townsville nurse Maria Sevilla and her son Tyrone, who have been in Australia for eight years, had a skilled working visa rejected by the Immigration Department because of her son's autism.

Tyrone was diagnosed in 2008.

The letter said Tyrone may be a burden on the taxpayer if he becomes a citizen later in life.

The Townsville Hospital nurse has appealed to the Migration Review Tribunal but it too has rejected the application.

Because the application was rejected they could be deported in 28 days.

"I hope I'm not considered as a burden. I'm trying my best to work for Tyrone's future," Ms Sevilla said.

"He loves to play under the sun. He was a bit fair when we came here to Australia and now he's like, brown skinned."

Queensland Disabilities Minister Coralee O'Rourke called it a "cold, heartless decision" by the Federal Government.

"I call on them to reverse the decision," she said.

Immigration Minister Peter Dutton said the family could go back to the tribunal and attempt again to sway its decision.

But Ms Sevilla said she hoped Mr Dutton would exercise his ministerial power and allow them to stay.

Ms Sevilla said she would not be able to give Tyrone the same quality of life in the Philippines.

"It's like, I'm pleading for our life, for Tyrone's future," she said.

The ABC has approached the Minister for comment.