Study director Dr Susan Morton said the guideline might be "setting mothers up to fail" when many returned to work within six months or found exclusive breastfeeding unrealistic for other reasons.
Dr Grant, the lead author of papers on iron deficiency in New Zealand infants, is also Dr Morton's associate director.
"We are working very closely with the Ministry of Health on this breastfeeding issue and other issues such as immunisation," he said.
Previous Plunket figures cited in the ministry background paper showed the national rate of "exclusive and full breastfeeding" to six months rising from 18 per cent in 2000 to 25 per cent in 2006.
Plunket national clinical adviser Alison Hussey said 16 per cent of Plunket babies were breastfed exclusively to six months in the last half of last year.
Dr Morton said these rates were not out of line with Growing Up in NZ, which found that 28 per cent of mothers breastfed exclusively until their babies were five months old - close enough to the ministry guideline of "around six months".
Dr Grant said premature, low-birthweight and fast-growing babies may need iron-fortified milk formula, baby cereals or iron supplements as well as breast milk before that time.
"I think we should say there are some groups for whom the guideline in its simplest form is not sufficient," he said. "My guess is 10 to 20 per cent of babies based on low birthweight, premature gestation and rapid gain of weight."
Health Ministry chief adviser for child and youth health Dr Pat Tuohy said premature or low-birthweight babies would almost certainly need iron earlier because they did not get it in the last trimester of pregnancy.
Is breast best?
* The Ministry of Health says a pure diet of breast milk is best for most normal-weight babies for the first six months.
* But mothers with premature, low-birthweight or fast-growing babies should seek medical advice about introducing soft iron-fortified foods sooner.