MAF is to look into whether it should have acted sooner after being told more than 100 calves were starving on a Waikato farm.
The calves had to be shot and were on a property owned by the Crafar family, who run New Zealand's largest family dairy business.
The Crafars have been prosecuted numerous times in the past, mostly for illegally discharging dairy effluent.
In the most recent case, the family was fined $90,000.
The Ministry of Agriculture and Forestry (MAF) says it was told about the calves on a Friday at the beginning of September but did not send an investigator until it got a second call the following Monday.
The investigator sent to the farm found a looming disaster, with some calves dead or dying, and others crying out to be fed.
A spokesperson for MAF, Greg Reid, told Checkpoint a decision on whether the ministry will prosecute for animal neglect will made by next week.
MAF will also look at its handling of the matter, Mr Reid said.
Farmer 'horrified' at calves' plight
Farmer Allan Crafar has admitted the calves were shot about three weeks ago at the farm near Benneydale.
Mr Crafar told Morning Report on Tuesday the manager at the farm had put a group of young people in charge of the calves, and obviously they were not competent.
Mr Crafar said he was shocked and horrified to hear of the animals' plight.
The family is currently trying to sell its 22 central North Island farms, claiming it is being hounded out of the industry by officials.
Fonterra says it will await the out-come of the MAF investigation before it decides whether it will take any punitive action against the farm owners, who supply it with milk.