Primary Industries Minister Nathan Guy said about $100 million was spent each year on border clearance for passengers and crew.
"In the past, these costs have been met by taxpayers. The Government considers it is fairer for the costs to fall on passengers traveling internationally," Mr Guy said.
The levy is expected to raise about $100 million a year, and will fully meet the costs of passenger border clearance by 2017/18.
The Government said the move would bring New Zealand in line with other countries including Australia, the United States, the United Kingdom, and China.
When combined with existing charges, the levy will be around $36 for a return journey, which the Government said was lower than Australia's passenger charge.
From early next month the public and industry will be able to give feedback on the proposed levies.
Budget 2015 also contains $25 million in extra funding over four years to aid biosecurity at the border.
Mr Guy said the investment would help improve New Zealand's import health standards to ensure they focus on the greatest risks, provide better auditing of other countries' systems, expand the use of detector dogs and increase the number of x-ray machines.
The discovery of fruit flies in Auckland earlier this year has put a spotlight on biosecurity measures, with Labour claiming that cuts to funding have led to lax border security measures.
It has vowed that Labour would return to 100 per cent screening of bags at airports.
An extra $4.7 million over four years will fund more Customs officers to screen departing passengers for threats such as terrorism and drugs.
Customs Minister Nicky Wagner said this would help maintain New Zealand's low-risk status and help international efforts to combat terrorism.
Total spending on Vote Customs will decrease by 8.4 per cent to $189,562,000 in 2015/2016.
