Approval for an airline to bring a passenger into the country was obtained through Immigration, which advised airlines whether a passenger was allowed to board or not.
Had Cathay Pacific provided the information, it would have been told not to board the Bahraini national, who has since left New Zealand.
This was the second time the airline had been prosecuted for not meeting its requirements under the Immigration Act, the agency's assistant general manager, Peter Devoy, said. "INZ takes this type of offending very seriously as airlines have a crucial role to play in maintaining the integrity of New Zealand's immigration system and keeping the border secure."
The maximum sentence for failing to comply with the act is up to three months' jail, a fine of $50,000, or both.
Mr Devoy said reasons people were refused entry included: not considered to be genuine visitors and failure to meet character requirements, such as not declaring serious criminal convictions, deportation or exclusion from another country.
Cathay Pacific's head office in Hong Kong told the Herald, "Cathay Pacific will review our procedures and strengthen communication with originating ports to prevent similar incidents from happening."
Hong Kong passport holders, at 115, were the highest number turned away, followed by South Africa (94), Great Britain (89), Taiwan (88) and Malaysia (85).
More than one in four, or 343, who failed to meet New Zealand entry requirements last year came on Air New Zealand. Other airlines with significant numbers include Qantas (157), Jetstar (115), Cathay Pacific (112) and Emirates (111).
But Air New Zealand spokeswoman Emma Field said the numbers did not "compare apples with apples".
"It is disingenuous to draw a direct comparison between those arriving on Air NZ services and those travelling on other carriers due to the fact that Air NZ accounts for the vast majority of visitor arrivals into the country.
"Despite carrying a significantly higher number of passengers into the country, [we have] fewer fineable infringements than a number of other airlines."
Airlines were slapped with 928 infringement notices last year. The highest numbers went to Latam, formerly Lan Chile (229), Qantas (163), Virgin Australia (134), Cathay Pacific (70) and Jetstar (64).
With 25 infringements, Air New Zealand is 10th on the infringement table. An Immigration spokesman explained that airline infringements were about airline non-compliance, while refused entry decisions were about passengers who presented immigration risks.