Department spokeswoman Heather Fairbairn says the document states that mill effluent will be measured at the end of an effluent transmission pipe, referred to as Point A.
But Fairbairn says the permit should have said the effluent will be measured at the outlet of an aerated stabilization basin, called Point C.
The department issued the industrial approval for the mill last Friday that requires tighter restrictions on emissions and water consumption.
But Northern Pulp has said it plans to challenge the permit, saying it threatens the mill's long-term viability.
Fairbairn says once the amended version of the permit is posted, there will be another 30 days granted for appeals to be filed.