Mr Guy said the changes, which airlines were consulted on, would strike the right balance between encouraging compliance with the law, and imposing a fair and reasonable cost on airlines that fail to comply.
"With more than 4.5 million people flying into New Zealand every year, it's important that we protect our borders and encourage compliance with the law," he said.
"Most airlines do a very good job of meeting their requirements, but we need to recognise the seriousness of not doing so. It can result in people entering New Zealand to work illegally, people trafficking, or costs to our health system."
The changes bring New Zealand in line with Australia, Canada, the United Kingdom and the United States, which all impose infringement fees on carriers.
Individual pilots would be fined only in cases where the owner, agent or charter company of the aircraft was not based in New Zealand - for instance, a private jet pilot flying passengers in for a visit.