A Chile-based airline has been prosecuted and charged more than $11,000 for allowing a passenger to board a flight to New Zealand, breaking government orders in doing so.

LATAM Airlines breached Immigration New Zealand's Advance Passenger Processing System, which advises airlines whether a passenger or crew member has the authority to travel to New Zealand.

The breach was in relation to a passenger from Syria who was incorrectly documented by a LATAM Airlines check-in agent in Santiago as being Brazilian in nationality.

The agent's mistake led to a "board with outward ticket" directive.

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Even though the worker was then informed by telephone and email from INZ not to let the passenger board, he was allowed to do so.

The passenger was removed from New Zealand the same day he arrived in November 2015.

At Manukau District Court today the airline, which was formerly called Lan Chile, was convicted and fined a total of $11,700 plus court costs for failing to comply with the airline's obligations.

Immigration New Zealand's national border manager Senta Jehle said it was the third time the airline had been prosecuted under the Immigration Act.

There had also been 590 infringement notices between July 2012 and May 2017 for breaching the same act.

Seven of these were related to failings to comply with a 'do not board' directive.

A spokesperson from LATAM said the company was "committed" to abiding by the laws and regulations in each country where it operates.

"As part of the company's ongoing compliance practices, it has since reviewed its internal procedures and staff training to avoid situations of this nature," they said.

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Jehle said the department took the offending "very seriously".

"Airlines have a vital role to play in maintaining the integrity of New Zealand's immigration system and keeping the border secure," she said.

Jehle said the airline left Immigration New Zealand no option but to take prosecution action.