CYF confirmed yesterday those babies were in their care.
"They are both safe and well with Child, Youth and Family caregivers," said CYF northern regional director Grant Bennett.
CYF refused to say whether the infants or their parents were known to the organisation. A spokeswoman said CYF would not comment further as police had asked them not to.
A source said the infants were siblings and are the children of the other couple who live with JJ's mother.
Detective Inspector Scott Beard said last week that the four adults were all at the house when JJ died and had given stories that conflicted with the findings of the post mortem examination.
Mr Beard said there were inconsistencies and urged the adults to tell the truth about what happened at the house the morning JJ died.
JJ was buried after a tangi in Kaeo, Northland, last week.
Relatives set up a tribute page for JJ on Facebook and spoke about his death over the weekend. They said the extended family did not know what had happened to JJ and wanted to make that clear.
"There were four in the home when this terrible thing happened and only they know what really happened," one wrote.
"I would just [like] to point out in all the cases of these poor children, a lot of the family members don't know what's going on. It's easy for us all [to] point the finger but until the truth comes out there's not a lot we can do. I also hope that justice is served to whoever did this to JJ."
Roxanne Ruhe, JJ's aunt, later wrote: "We are doing everything we can to find the truth."
A friend of JJ's aunt wrote a heartfelt message: "My heart goes out to little baby JJ and to all his loving family. His aunty, my precious friend, I wish I could take your pain away."
