In a statement yesterday, Dr Jan Wright said the risk to the water quality of the area was of such significance that the applications should be called in.
She wrote to Dr Smith this week asking him to call in the applications for effluent and air discharges.
She was particularly concerned about the effect of the operations on the water quality of the Ohau and Ahuriri catchments.
The proposals from three companies - Five Rivers Ltd, Southdown Holdings Ltd and Williamson Holdings Ltd - involve establishing 16 dairy farms, with up to 17,850 cows housed in cubicle stalls.
Submissions close today for the Williamson Holdings development.
Dr Wright said the combined effluent of the operations would be similar in quantity to that produced by a city the size of Christchurch.
A recent report from the National Institute of Water and Atmospheric Research suggested if the amount of nutrients entering Lake Benmore was to substantially increase, then the water quality of the lake and lower Waitaki River would probably deteriorate seriously.
Such a result would be "highly undesirable", especially as the region was popular for tourism and recreation, Dr Wright said.
In her report Change in the High Country: Environmental Stewardship and Tenure Review, she recommended the minister should call in development applications that were proposals of national significance because of their potential for significant adverse effects on lakes or outstanding landscapes in the high country.
"These proposed dairy farms are just the kind of development I envisaged when making my recommendation," she said.
Last week, Dr Smith said the Government recognised the level of public interest in the proposals and was considering intervening.
The ability to use call-in powers was constrained by the fact the animal welfare issue over housing the cows lay with the Animal Welfare Act, rather than the Resource Management Act, and also because the applications were lodged before the Government's improved resource management procedures come into effect on October 1, he said.
