Baby experts are calling on the Government to fund a "quick, cheap and safe" screening tool which could pick up hundreds of newborns with potentially deadly heart defects each year.

In today's New Zealand Medical Journal, researchers say a national newborn screening programme - based on testing with a device called a pulse-oximeter - is desperately needed to identify serious heart conditions in babies before it's too late.

"We know this programme will save lives. Some hospitals are already using this tool but a national programme needs to be introduced to ensure inequities between district health boards are not accentuated," study leader and director of the Liggins Institute Frank Bloomfield said.

The Ministry of Health said it was developing national guidelines for pulse oximetry which were expected to be completed by June.

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"The cost of establishing and operating a new national screening programme for newborn pulse oximetry screening has not yet been determined," a spokesperson said.

A small, band-aid like device is strapped around the baby's foot, which indicates the oxygen level in their blood. If the oxygen level is low (normal levels are 95 per cent or more) it could indicate critical heart defects and in these cases urgent surgery is carried out.

"It is quick,cheap and safe," Bloomfield said.

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He said the test could save four babies who die from heart defects each year and would pick up about 200 newborns with the serious disease.

The test takes about five minutes and costs no more than $4, Bloomfield said.

Each machine costs about $1300 and was expected to last 10 years.

Babies are already screened, before or after birth, for a number of conditions, including hearing problems, metabolic disorders and Down's syndrome.

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Congenital heart disease affects about one in 100 babies in New Zealand, although some conditions are not diagnosed until adulthood.

Less than half of infants with critical congenital heart defects are diagnosed prior to birth, and 20 per cent are diagnosed after discharge from hospital - which Bloomfield said can often be too late or develop into a more serious condition than if it was picked up earlier.

Bloomfield said his team recommended that the testing needed be done between two to 24 hours after birth.

"The issue we are trying to detect is a critical heart disease that is time dependent in that the sooner you pick it up the more likely it is that the baby will remain well and the intervention will be successful.

"If you don't pick it up quickly then that's when the baby runs the risk of becoming exceptionally unwell, or even dying."

New Zealand College of Midwives adviser Lesley Dixon said the college supported the calls for a national screening programme as the benefits had been proven but said it needed to be well resourced.

"It would be midwives doing majority of the screening so the time and cost of the equipment needs to be considered."

These calls follow a screening trial which found some newborn babies missing out on screening because of unequal access across DHBs and populations. The main causes were midwife shortages, overworked midwives, and failure to register with a maternity carer.

Midwives had roughly 20 tasks after the birth of the baby, and their assessments took between two and three hours.

The test is already routinely done at five New Zealand hospitals, including the Auckland City, Wellington and Dunedin hospitals, and at the three community birthing units in Counties Manukau.