The study found European-mother/non-European-father couples were more than twice as common as the reverse combinations for babies with European and either Tongan, Tokelauan, Samoan, Niuean or Middle Eastern parents.
Similar, but slightly smaller biases showed up for European relationships with Cook Islanders, Fijians and Africans. European-Asian relationships were even more lopsided in the opposite direction.
The most common inter-ethnic combination in New Zealand, European/Maori couples, showed a weaker bias in the same direction than European/Pacific couples - 33,500 babies born in the five-year period had Maori fathers and European mothers, compared with 27,400 with European fathers and Maori mothers.
New Zealand has one of the world's highest rates of ethnic intermarriage, reflecting our diverse demographic mix.
At the last Census 79 per cent of people said they were European, 15 per cent Maori, 9 per cent Asian, 7 per cent Pacific and 1 per cent others - a total of more than 100 per cent because many had more than one ethnicity.
Last year almost 30 per cent of "Asian" babies, about 33 per cent of "European" babies, 51 per cent of "Pacific" babies and 69 per cent of "Maori" babies were registered as having at least two ethnicities.
This mixing is happening quickly. The proportion of Maori mothers who were of solely Maori ethnicity fell from 67 per cent in 1996 to just 49 per cent last year. Pacific mothers who were solely Pacific fell from 82 per cent to 74 per cent.
Dr Didham found there was surprisingly little evidence of racism, because almost all parents registered their babies as having the ethnicities of both parents - not just the one from the country's dominant European group.
However, the exceptions were couples where one partner came from the Middle East, and to a lesser extent from Fiji or Africa.
"The biggest difference in retention was for NZ European/Middle Eastern parents with 95 per cent of children recorded as NZ European and only 77 per cent recorded as Middle Eastern," Dr Didham said.
"Over the last decade for some groups, racial profiling and border security checks have reinforced discrimination."
Another indicator came from the 2200 babies over the five years whose parents recorded their ethnicity as "New Zealander". Four-fifths had at least one parent, believed to be European in most cases, who also described their ethnicity as "New Zealander", but in the other cases neither parent called themselves "New Zealanders".
A third of the "New Zealander" babies with no "New Zealander" parents had Asian parents. A further 10 per cent had Middle Eastern, Latin American or African parents, even though such parents accounted for only 2 per cent of all births.
Dr Didham found that fathers were on average three years older than mothers.
PERFECT MIX FOR MAKA FAMILY
It was the Afro haircut that caught the young girl's eye when a Tongan rugby player called Melino Maka turned up in the Manawatu town of Shannon.
Mr Maka and his adoptive brother, who had moved there first as a manager for a wool scouring plant, were the only Tongans in town.
The girl, who has been Lyn Maka for 32 years now, says her parents were taken aback when she started dating the younger Tongan with the Afro, whom she met through rugby.
"They like him now," she says. "They thought he was all right."
But her husband adds,"Back then it was a challenge."
Birth data shows that Tongan/European couples are more likely to be European female/non-European male combinations than any other ethnic group. There were 1404 babies born to Tongan fathers and NZ European mothers between 2006-2010, 166 per cent more than the 527 babies born to NZ European fathers and Tongan mothers.
Mr Maka's own brother also married a European woman and the Makas know several other male Tongan/female European couples. They also know some in the reverse order.
When their three sons were born, they registered their ethnicities as both European and Tongan. Their eldest, who sadly died young, was particularly proud to be Tongan.
"The other two identify as Tongans but not actively," Mrs Maka said.
Mr Maka, who chairs the Auckland Tongan Advisory Council, said his biggest regret was that he did not teach the boys the Tongan language.
"We lived in an area where we hardly saw any Tongans unless we went to Palmerston North, and even then there were hardly any, so I didn't think at the time that it was necessary."