"Significant animal welfare issues" have been found among the 20,000 cows on the 22 farms owned by the Crafar family, the Ministry of Agriculture and Forestry (MAF) says.
On some farms, MAF had given "explicit directions" for fixing problems such as underweight animals with underlying health issues, inadequate feed, overstocking,and lack of shelter for calves, MAF director-general Murray Sherwin said.
Agriculture Minister David Carter last week ordered urgent welfare checks on the Crafar farms.
Mr Sherwin said animal welfare inspectors, helped by Food Safety Authority veterinarians and industry organisations, had visited all Crafar properties.
Input from veterinarians and farm consultants had been organised.
MAF said last week it would announce whether there would be prosecutions over treatment of 100 calves on a Crafar farm at Benneydale in the Waikato, where animals were dying because workers did not teach the calves to drink from a trough.
But Mr Sherwin said it would take time before specific prosecution decisions were made.
"While on-farm inspections have been completed, and some serious animal welfare issues identified, investigations are ongoing and evidence is still being gathered," he said.
A Crafar family member has separately said that on many farms the family relied on sharemilkers or herd managers to look after the day-to-day operations.
Receivers Michael Stiassney and Brendon Gibson of KordaMentha were this week called in for four Crafar family companies - Plateau Farms Ltd, Hillside Farms Ltd, Tararua Farms Ltd, and Ferryview Farms Ltd - which own the bulk of the Crafar interests.
Mr Sherwin said MAF and the Crafar farm receivers would continue to collaborate and stabilise the operation of the properties.
The Reporoa-based Crafar family, grew its original property to 22 farms with 20,000 milking cows, 10,000 other stock, 200 staff and an estimated $200 million of debt to Westpac, Rabobank, and PGG Wrightson Finance.
Mr Stiassney said when he took over on October 5 that his initial concerns were to protect animal welfare.
The current cold snap was raising "pressing issues" around making sure animals received adequate food and shelter.
Mr Crafar has claimed that he, his wife Elizabeth, and his brother Frank were being unfairly targeted over issues such as dirty dairying and animal welfare.
The death of the Benneydale calves came on top of convictions for animal neglect at a Crafar farm in Hawke's Bay in 2006.
