Nearly a third of public submissions to the Government's flag consideration panel, all of them critical of the process and supporting the current ensign, were ignored in official reports and advertisements purporting to show public opinion.
Labour Party MP Trevor Mallard said the revelation showed the process was suffering from "total spin" and the panel was pushing to change the flag in breach of its mandate to be neutral.
The discounted submissions were revealed following analysis of more than 26,000 online submissions to the "stand for" campaign run by the flag panel from May to July.
Conducted by software consultancy firm Entopix, the analysis is published today on new data journalism site Herald Insights.
Entopix principal Alyona Medelyan, who has a doctorate in natural language processing, said the results were unexpected as the wordclouds published by the flag panel varied markedly from what raw data showed.
She said more than 8000 comments expressing disapproval with the flag change process or support for the current flag, nearly a third of total online submissions, seem to have been ignored.
Ms Medelyan said her analysis showed the resulting wordcloud, which appeared to rely on counting comments rather than a more sophisticated measuring of themes, wasn't a fair reflection.
"They certainly tweaked the analysis to fit what they wanted to display," she said.
While the official wordcloud put out by the panel claimed "equality" was the most prominent reply in submissions seeking to determine what New Zealand "stands for", the analysis showed this was mentioned only 1272 times.
In comparison, 8315 submissions called for the current flag to be kept, and 5026 claimed the $26 million process was a waste of money. Neither of these opinions were recorded in the flag panel wordcloud.
Mallard said the discounting of these opinions was disappointing.
"That, frankly, is a level of dishonesty that I would not expect from a government-appointed body," he said.
Suzanne Stephenson, head of communications for the flag panel, rejected any suggestion of spin and said the wordcloud was never claimed as "statistically significant".
She said the thousands of discounted submissions were ignored as they didn't answer the question of "what was important to New Zealand" and debate about the current flag was "outside the panel's remit".
She said the "stand for" campaign may have been misconstrued by thousands of submitters.
"I think people misunderstood it as a polling exercise. But it's very early in the day, and that's what the referendum is about. Your official voice is counted there," she said.
Deputy Prime Minister Bill English, who is overseeing the flag change referendum, said in a statement that the process was a delivery of an election promise but the collection and assessment of submissions on the flag was not his responsibility.