The number of Malaysians refused entry "appears to simply be a matter of our geographic proximity to Malaysia", an Immigration spokeswoman said.
Travellers with Malaysian passports are allowed to enter New Zealand without visas.
Malaysian Immigration says the country is being used as a transit point by syndicates which issue fake passports to help people to enter countries that have visa-free arrangements with Malaysia.
More than 50 per cent of the travellers stopped at the border in 2011/12 were considered likely to work illegally or overstay.
"People who arrive at the border having been profiled as meeting an element of immigration risk are interviewed to determine their bona fides," said the spokeswoman.
Immigration NZ also works with other border agencies such as Customs and the Ministry for Primary Industries in all of New Zealand's international airports.
Those officers often uncover items, such as tools of the trade or CVs, in a passenger's luggage indicating the person is planning to work illegally. .
"The decision to refuse entry can be based on, among other things, their immigration history, the immigration history of any family members, the information they provide at the interview and intelligence we may have from other agencies or countries," the spokeswoman said.
Such intelligence-sharing has led to suspected criminals being stopped at the border.
A group of seven Romanians were red-flagged when two of them, a couple, were identified as part of an earlier group denied entry in 2009 after being unable to satisfy officials they were travelling for legitimate reasons.
The couple were flying from Romania to Auckland via Istanbul and Singapore in September.
An Immigration officer established five other Romanians on the same flight bought their tickets from the same travel agent on the same day.
Several members of the group had previously been deported from the United States where they were involved in thefts involving tens of thousands of dollars.
In April, nine suspected card skimmers carrying Bulgarian passports were stopped from entering New Zealand after a border security officer in Auckland linked two people to an ATM fraud in Mexico.
Closing the door
Numbers turned away at border in last five years:
Malaysia 333
Brazil 193
S Korea 165
Hong Kong 122
S Africa 122
Romania 111
Reasons for refusal 2011/12:
*Non-genuine reason for travel 396 (50.1 per cent)
*Other, including lack of funds and health concerns 278 (35.2 per cent)
*Character 80 (10.1 per cent)
*Visa issues 25 (3.2 per cent)
*False documentation 7 (0.9 per cent)
*Minor accompanying referred adult 4 (0.5 per cent)