Chief executive Stephen Parry said the council has instigated an urgent review of security and fencing at the ponds.
"The relevant authorities have been notified and we will work closely with them."
A Gore District Council spokeswoman said the two large ponds, which are between Grasslands Rd and the Mataura River, are fenced.
Police were alerted that the child was missing at 9.30pm last night.
At that stage family, friends and neighbours had already begun searching for the boy.
Police and LandSAR started a land search in the area and located the young boy unresponsive in a pond about 11.15pm.
He was unable to be resuscitated.
Police have thanked those volunteers and neighbours who assisted in the search.
"Our condolences are with the family who have asked for privacy at this time," police said.
Police would be making inquiries today on behalf of the Coroner.
Additional reporting: Otago Daily Times