Brown made one cut to the flood bank using a digger which also allowed silt and sediment into the Waiotu River.
He told the Northern Advocate he would not cut the stop bank again.
"I thought there was a provision that protects you under certain circumstances because stopbanks have been opened up in the past," he said.
The fine, he said, was "tough" considering he was paying about $20,000 a year in targeted rate for the scheme. Brown's family trust owns a dairy farm on State Highway One, Waiotu, which is also protected by the scheme.
He used a digger to cut through the stopbank and as a result, flood waters were discharged to the Waiotu river.
WDC investigations revealed Brown had cut the stopbank and notified NRC.
An abatement and an infringement notice were issued by NRC to Brown's company.
In explanation, Brown said he cut the stopbank because his house was flooded. The cut was about 4m high and 9m metres wide at the top and 2m wide at the bottom.
Brown later arranged for a contractor to repair the first cut to the stopbank and repairs were completed in early July. On July 29, he helped WDC repair the second cut by providing a tractor and a digger.
Lammers, who made two cuts to the stopbank, admitted to two charges laid by the Northland Regional Council and was fined $45,000.
His family owns two dairy farms at Forsythe Rd and Hukerenui Rd which are protected by the scheme. The farms are situated in a pocket known as Te Mata.
In a phone call made by NRC monitoring programme manager for water and waste, Tess Dacre, to Lammers, the latter admitted he cut the stopbank on July 14 and 15, 2014.
"I did cut the banks. I am pretty much screwed anyway," he said.
The banks were repaired by WDC engineers in summer when conditions were suitable.