Home Affairs Minister Peter Dutton is talking down the prospects of intervening in the case of a mother who fears being torn apart from her son if she is deported from Australia.

Bernadette Romulo has lived in Australia for the past 11 years but her application for permanent residency has been rejected.

Ms Romulo fears she and her two daughters, aged 12 and 13, will be forced back to the Philippines within days.

However, her eight-year-old was born in Australia to an Australian father, who has partial custody.

Ms Romulo said she and her daughters would be devastated if they had to leave Australia, describing her predicament as every mother's worst nightmare.

"My boy cries himself to sleep every night and is having nightmares, knowing we will soon be leaving him behind," she wrote in an online petition signed by more than 18,000 people.

"Please, I'm begging Minister Peter Dutton to let me and my son stay together. Please don't take my son away from me."

Mr Dutton was reluctant to comment on the case when asked about it in Canberra on Monday.

He acknowledged there were some cases involving children where he did intervene.

But he said there were others, including some subjected to lengthy court battles, where protection was not found to be owed and he had decided not to act.

"People have been given ample notice over a long period of time to prepare themselves to depart, they refuse to depart, then try and string it out through a pointless exercise through court," he told reporters.

"But nonetheless it delays their departure, and then they try and make it look more acute at the end stages."

Mr Dutton urged people to cut through emotions and cases attracting "cheap TV" to look at the facts.

"We have those tough decisions to make but as I say we act compassionately in many, many cases that I sign off on each week," he said.