NRC harbour master Jim Lyle said the council did not see any legal basis to his counterclaim.
Prior to the Environment Court judgment, NRC issued Mr Philbrick with two abatement notices in 2010 and another in 2013 for anchoring his 18-metre ketch, Rose Maree, in different places in the Whangarei Harbour for longer than permitted under the Regional Coastal Plan.
The plan stipulates vessels must not anchor in coastal waters within the same embayment, inlet or estuary for more than 14 consecutive days except where anchorage for a longer period is necessary due to bad weather, accident, or emergency.
Designated areas such as marina berths are an exception.
The plan also says anchored vessels should not be in a position that interferes with the safe navigation of other vessels.
There is nothing in either the plan or the Resource Management Act that refers to the Whangarei Harbour as an estuary.
However, the NRC has accepted an interpretation by the National Institute of Water and Atmospheric Research (NIWA) that the entire harbour from Marsden Point to Lord Point was an estuary.
"My interpretation of the Whangarei Harbour is it's a large harbour with lots of embayments and that's why I kept moving my ketch to Urquharts Bay, Parua Bay, Limestone Island, and the Bay of Islands before the 14 days were up," Mr Philbrick said.
"I don't have a problem with the 14-day rule. The designation of the harbour as an estuary was never mentioned until NRC decided to prosecute me which was unfair."
Mr Philbrick said he first learnt the harbour was an estuary during the Environment Court hearing in April 2015.
Since being made aware of the 14-day rule by an NRC staff in 2008, he said he had abided by it.
Mr Philbrick said despite spending a lot of time in different areas of the Whangarei Harbour, he did not want to buy a mooring spot and said NRC could not force him to.
He said he would be forced to borrow money if NRC eventually won the legal stoush.
Mr Philbrick and his father, Brian, have chosen to live onboard the Rose Maree and to sail round the country. It took them six years to build the ketch on Waiheke Island and then Tangiteroria before they launched her in 2006.
Mr Lyle said boaties generally knew where to anchor in the harbour and for what duration.
Officers also educated them through visits, he said.
Monthly berths at the Town Basin cost between $650 and $1290, inclusive of power and water. The charge for berths without power and water is between $275 and $460.