It was not enough that Ms Lee's case might be weak or the decision was to be made on a fine balance of evidence, he said.
She applied for a building consent for the house in August 2006, and it was granted in October.
Work began in January 2007 and council staff carried out a number of inspections.
The house failed the final inspection in March 2008, and the council sent a notice for her to address a number of matters with spouting, internal and roof gutters, and rainwater heads.
In its application for summary judgment, the council said Ms Lee knew the house had been built with significant defects and its construction did not comply with the New Zealand Building Act and the Building Code.
The defects resulted in a loss of value, it said.
Ms Lee's decision not to file a claim under the Weathertight Homes Resolution Services Act 2006 showed she knew the defects reduced the value of the house, the council said.
Judge Bell agreed, saying the council had shown by a strong margin that Ms Lee discovered damage to her house before May 21, 2008.