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The woman was removed from her family by CYF and sent to live with her uncle in 2001 when she was 16.. Her uncle had been to prison for six years before the placement for his part in a gang rape.
She says her uncle and a friend both abused her while she was in his care. Now 27, she is HIV positive and has passed the disease on to her first-born son.
Ministry deputy chief executive David Shanks said it wasn't mandatory for criminal checks to be done around family placement in 2001.
"In hindsight it would appear we didn't do enough of a good job around this and we let Joanne down."
Green Party co-leader Metiria Turei has weighed in on the debate, demanding CYF fronts up and tells the public whether it is undertaking mandatory checks of all family placements.
Mr Shanks said: "I can assure the public that our assessment process has been strengthened in the most recent years, with staff expected to do police checks if there are any concerns about family/whanau placements."
He said it became mandatory to do criminal checks earlier this year.
"(The woman) should never have gone to live with an uncle who was a convicted rapist and we are very sorry about what happened to her."