But the Ministry of Health and Children's Commissioner Dr Russell Wills are standing by the official guidelines. Dr Wills said Dr Morton's comments reflected a classic "authority's dilemma".
"What should authorities advise when what good science says is best for baby is not what most parents do?" he asked.
"If you compromise and say that something is fine when it's not, you are misrepresenting the science and selling parents short."
The Health Ministry's chief adviser for child and youth health, Dr Pat Tuohy, said breast milk was optimised for infant development and changed as the baby grew.
It also minimised obesity because babies drank only what they needed.
The multi-million-dollar Growing Up in NZ study is New Zealand's first large-scale study following a group of children through their lives since two studies that began in Dunedin and Christchurch in the 1970s.
Infants in the new sample were born in Auckland and the Waikato between April 2009 and March 2010.
Results released today show that breastfeeding has increased dramatically over the decades, from 55 per cent of the Dunedin sample who were breastfed at any time to 97 per cent in the latest group.
But the numbers breastfed "exclusively" - meaning "no other substance apart from breast milk and prescribed medicines from birth" - dropped steeply to 81.7 per cent at one month, 63.4 per cent at three months, 28.1 per cent at five months and 6 per cent at six months.
The director of breastfeeding support group La Leche League, Alison Stanton, said more and more women were wanting to breastfeed their children exclusively for the first few months of their lives, but there were reasons many stopped.
"There are many barriers to women who have the goal to breastfeed. There are societal issues, growing up in a bottle-feeding family and just going back to work can lead to women stopping."
The official Health Ministry guideline, in line with World Health Organisation advice, is: "Exclusively breastfeed your baby until your baby is ready for and needs extra food - this will be at around six months."
Dr Morton said the finding that most mothers ignored this advice raised two issues.
"The first one is: is it appropriate in New Zealand to be reliant on WHO guidelines for exclusive breastfeeding that are based on countries where sanitation and water quality are not good?" she asked.
"If you are thinking about sub-Saharan Africa, that is the best way to prevent infections and gastroenteritis in your children. In New Zealand, sanitation and water quality are different, so the provision of something other than breast milk is not as dangerous.
"Secondly, how does that fit with an increasing trend for mums to return to work where, if you are exclusively breastfeeding, that creates significant challenges?"
Three-eighths (37.4 per cent) of the study's mothers were back in paid work nine months after giving birth. Half of those (18.7 per cent of all mothers) went back within 20 weeks.
Some, such as Human Rights Commission adviser Marama Davidson who returned to work six to eight weeks after having each of her six children, had a private room where she could express breast milk several times a day at work and a fridge to store it in.
But many working mothers could not do that.
"So maybe it just challenges us - are we setting them up with an expectation where most of them are going to fail?" Dr Morton asked.
The study also found that 52 per cent of Kiwi babies watch children's TV at least once a week by the age of nine months, and Dr Morton said interviews now under way at age 2 found that many are using iPads and other touch-screen devices despite official advice of "no screen time before 2".
