Although the study was carried out on animals, researchers at the University of Texas Health Science Center said the the same findings are relevant for humans.
They said that non-human primates used in the lab who ate less while pregnant impaired their foetus' brain development.
"This is a critical time window when many of the neurons as well as the supporting cells in the brain are born," Peter Nathanielsz, one of the researchers, said in a statement.
The team compared two groups of baboon mothers at Southwest Foundation for Biomedical Research (SFBR)'s private research centre.
One group was allowed to eat as much as they wanted during the first half of pregnancy, while the other group was fed 30 percent less.
They found decreased formation of cell-to-cell connections, cell division and amounts of growth factors in the foetuses of mothers fed a reduced diet during the first half of pregnancy.
"We found dysregulation of hundreds of genes, many of which are known to be key regulators in cell growth and development, indicating that nutrition plays a major role during foetal development by regulating basic cellular machinery," said Laura Cox, one of the SFBR scientists.
Previous studies have shown that marked nutrient restriction, such as in famine conditions, adversely affects foetal brain development.
Nathanielsz said that foetal nutrient deficiency was a special risk for both teenage mothers and women who get pregnant later in life.
"This study is a further demonstration of the importance of good maternal health and diet," said senior author Thomas McDonald.
"It supports the view that poor diets in pregnancy can alter development of foetal organs, in this case the brain, in ways that will have lifetime effects on offspring, potentially lowering IQ and predisposing to behavioral problems," he added.
The study also challenges the widely held view that mothers can protect their unborn babies from poor diets in pregnancy, he said.The findings are published in the journal Proceedings of the National Academy of Sciences.