A change to allow him back to the house where the child lived was opposed by Corrections and Police.
A district court judge asked CYF for a report that assessed the risks if the boyfriend was allowed to live with the children at the house.
At the September family meeting that a CYF staff member told the family that the report provided was "poor", Radio New Zealand reported.
"All I'm saying is the information that was given to the judge didn't actually concentrate and focus on the issues that we know that were happening in the home."
After the bail conditions were changed to allow the man back to the home, CYF followed up with a safety plan for the toddler and his sister, but there was no follow-up to make sure the child's mother and boyfriend stuck to it.
Soon afterwards the toddler was taken to hospital with injuries including a thigh fracture. An examination revealed injuries including a broken tooth and crushed fingers.
Hospital staff were concerned and warned CYF the toddler's mother was a suspect. At this time the toddler's sister was at home with the boyfriend - something not allowed under CYF's safety plan.
Despite the concerns, CYF and Police agreed the boy should be discharged back to the family home. In the secret recording, the CYF manager could not explain to the family why this happened, Radio New Zealand reported.
However, the manager said that CYF had fulfilled its statutory duties.
Legislation that in December passed its first reading will clear the way for the second stage of major state care reforms that will replace CYF with a new Ministry for Vulnerable Children, Oranga Tamariki.
Labour's Children's spokeswoman Jacinda Ardern said mistakes would be made so long as CYF was left as "brutally under-resourced" as it currently was.
"Whether it is things as basic as lack of proper supervision for new graduate staff...not to mention the fact they are not filling vacancies."
Ardern said she had no confidence that would change under the new Ministry for Vulnerable Children.
"You can never prevent mistakes when one of the obvious factors is you have staffing that is under an enormous amount of pressure."
Jan Logie, Green Party spokeswoman for social development, said CYF were clearly stretched and overworked, and that was costing lives.
"This is a life lost unnecessarily. For there not to be changes prompted by that actually just really stinks."
Logie said the Government had known for a number of years that more frontline social workers were needed, and for case loads to be lightened.
Social Development Minister Anne Tolley has been approached for comment. She has previously said extra resourcing had been announced to help overhaul care and protection, and more specialised staff would be employed in the new Ministry for Vulnerable Children.
Budget 2016 invested $347 million for cost pressures and to help transform the system, Tolley said.
