Court officials carrying out an eviction order on Tuesday discovered the bodies of an 11-year-old boy and a 14-year-old girl.
Police did not name the woman but said the bodies were wrapped in the same plastic bag.
Two of the woman's other children, aged 11 and 17, were found at a neighbour's home and placed in protective custody.
A post-mortem examination has been scheduled to determine how the children died.
Police Chief James Craig called it a "terrible find".
Tori Childs, a neighbour, told the Associated Press that she hadn't seen the two dead children for about a year.
Neighbours said the 36-year-old mother was behind on her rent on her three-bedroom apartment and was "going through some things".
A Detroit mother has been arrested after officials found two of her children dead inside her freezer.