The charges were brought to court by the Civil Aviation Authority.
In his ruling, released on Friday by the Queenstown District Court, Judge Phillips said: "I am satisfied that the defendant ... was careless in his manner of operating the aircraft.
"The defendant ignored the mandatory requirements and, in their place, used his planned self-designed contingency. I have found against him on this issue."
The judge also said the facts he had found established "clear fault" on the part of the pilot. Of concern were a "don't sink" alert from the cockpit at 700ft (213m) and a "bank angle" alert after the pilot had corrected the aircraft.
"Each one is on its own some concern, taking into account the nature of the aircraft and the surrounding terrain and the proximity of Lake Wakatipu ... The safety margins at the time were, in my decision, seriously impacted on."
Pacific Blue said it had received the judgment and was reviewing it.