The charity Save the Children monitored the health of children under the age of five for several months and found that almost half of them were acutely malnourished.
In remote areas, this figure could be even higher. Often, the children also suffered from life-threatening illnesses like pneumonia, malaria and diarrhoea.
"For some cases this may be the second or third time they have fought malnutrition, so their immune systems are already severely weakened," said Ben Foot, Save the Children's Nigeria director.
Region in turmoil
Islamist terrorist group Boko Haram's insurgency, which started in 2009, sparked a humanitarian crisis the UN called the worst in Africa.
The militants drove farmers away from their fields, which led to food shortages in Borno State.
Figures from the World Health Organization show that more than two million people have fled their homes, while seven million need humanitarian help.
"The international community needs to wake up to the scale of the crisis unfolding in north-east Nigeria," Foot said.
Donors pledged half a billion dollars in aid funds this year - but only one third of the money has actually been delivered. Foot warned that double the amount was needed next year to bring the situation under control.
mrk/mc (dpa, Save the Children)