"Malaysia Airlines was convicted of the first offence and would have faced a fine if it had come up before the courts again in the following 12 months," she said.
"The airline was fined $5500 in relation to the second prosecution."
In the 2012 incident, a Malaysia Airlines check-in counter employee altered the passport number of a passenger to help circumvent New Zealand's security systems.
In March of this year, two passengers travelling on stolen passports were also able to board the airline's Kuala Lumpur to Beijing flight MH370, which disappeared with 239 people on board and is still missing.
Most of the airline infringements related to passenger information requirements not being met or airline staff failing to check outward ticket requirements, Ms Dixon said.
"Immigration New Zealand uses a combination of electronic and physical profiling, as well as staff expertise, knowledge and experience to protect New Zealand from people who pose a risk or are otherwise not eligible to enter the country," Ms Dixon said.
Immigration's Advanced Passenger Processing (APP) system electronically confirms a passenger's entitlement to travel to New Zealand.
There would be an alert if a passenger did not hold a valid visa or if the passport presented was recorded as being lost or stolen.
Aviation expert Peter Clark said airlines faced a multitude of challenges when it came to processing passengers.
Sometimes visas were issued incorrectly and this couldn't be picked up until people arrived in New Zealand, he said.
"It's a real grey area. There's so many things that you could be denied entry at the border [for] - they could have been turned back at the border here because Immigration may have felt they didn't meet the criteria of their issued visa, did they declare a criminal record and when they got here was it found?
"This happens all over the world," he said.
"The problem is we've got so many different airlines flying into New Zealand from different parts of the world that have less stringent requirements."
Airlines tried their best to comply with regulations, but problems like human error or fraudulent passengers were often difficult to pick up and unavoidable, Mr Clark said.
Over the 12-month period, 1743 people were stopped from boarding New Zealand-bound flights and 1026 were refused entry when they arrived at the border.
Air New Zealand carried the highest number of people who were refused entry, and had the most people who were denied boarding.
Malaysia Airlines had 69 passengers who were denied boarding and 27 turned away upon arrival.
Ms Dixon said airlines had to provide APP data for everyone travelling to New Zealand, comply with boarding directives and ensure passengers had correct travel documentation before boarding.
"Under a new fines regime introduced in July 2012 infringement notices may be issued for breaches of these obligations and provide an alternative to prosecution action."
Air New Zealand spokeswoman Emma Field said it was "disingenuous to make direct comparisons" between airlines because, as a national airline, it carried a significantly higher number of passengers into the country.
"We have a very high APP compliance rate relative to the number of passengers we carry, in fact we account for just 3 per cent of total fineable infringements issued by Immigration New Zealand," she said.
Virgin Australia spokesman Luke O'Donnell said the airline had strong protocols in place regarding compliance with regulations.
"We are aware that the infringements during the financial year were higher than normal and this is currently being addressed," he said.
Malaysia Airlines could not be reached for comment last night.
