The company flies ministry inspectors to Japan so they can inspect and decontaminate the cars before they leave for New Zealand.
This means the cars are cleared when they arrive here without further detailed inspection.
In return, Kiwi Car Carriers pays for the inspectors' international and domestic air travel, accommodation, office space, cellphone calls, meals, insurance and other "reasonable" living expenses.
Rival car shipping company Armacup Maritime Services, which has been fighting to get MAF to end the deal, said it was prompted to reveal the deal after New Zealand Herald reports of a similar arrangement between Customs and the corporate jet company Sky Care.
That deal allows Sky Care's corporate customers, arriving on private jets, to go through a VIP customs check in the company's offices instead of the usual process at the main terminal of Auckland Airport.
Armacup's lawyer, Peter Thorp, said MAF was a Government regulatory body which should not be making exclusive deals with private companies.
He said the deal also created the potential for harm to the New Zealand environment.
The cars might be left on the docks in Japan for a time after being inspected and before being loaded, he said.
During this time they could pick up organisms which could go undetected on arrival here if there was no further inspection.
Kiwi Car Carriers' New Zealand manager, Terry Riches, said the company was very concerned about protecting the environment and making sure any risks were managed overseas.
He said that before the contract was signed in December 1997, Armacup and other companies had been given the same opportunity as Kiwi Car Carriers.
"However, to this day none has taken up the option."
MAF's director of forest biosecurity, Dr Ruth Frampton, said all car importing firms had the opportunity to get cars inspected overseas or in New Zealand.
While Kiwi Car Carriers was the only one having inspections overseas, MAF did not have an exclusive deal.
Dr Frampton said there were equal risks of infestation whether the cars were checked here or in Japan. In Japan the cars were not usually sitting on the wharf for more than 12 days after inspection.
She said infestation within that time was unlikely.