The woman, who is not the children's biological mother, is understood to be in a de facto relationship with the father of the children.
The couple went out of the country and left behind their children at their home alone. The woman was arrested when she flew into Perth airport on Thursday, The Daily Telegraph reported.
She has been charged with two counts of having the care and control of a child engaged in conduct knowing that conduct may result in harm to the child, the report said.
Child Protection Minister Andrea Mitchell said she was "horrified" by the allegations.
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"When I first heard about this situation, I was horrified. Any incident... Where there is children of any age being left alone is extremely concerning," Mitchell said.
Western Australia Police said the children were found alone at a Cloverdale home when officers gained entry through an unlocked door.
Police allege the children had been left home alone since Tuesday.
"It will be alleged both parents were overseas at the time the officers entered the property. The children were subsequently removed from the property and placed into appropriate care," police said in a statement.