Tens of thousands will die if treatment does not reach them soon, Unicef warns.
In areas where Boko Haram militants had been in control, it found people without water, food or sanitation.
Last month, a charity said people fleeing Boko Haram had starved to death.
The Islamist group's seven-year rebellion has left 20,000 people dead and more than two million displaced.
Nigeria's military is involved in a large-scale offensive against the group.
Unicef says that as more areas in north-eastern Nigeria become accessible to humanitarian help, the extent of the nutrition crisis affecting children is becoming more apparent.
It said that of the 244,000 children found to be suffering from severe acute malnutrition in Borno, almost one in five would die if they were not reached with treatment.
"Some 134 children on average will die every day from causes linked to acute malnutrition if the response is not scaled up quickly," said Manuel Fontaine, Unicef's Regional Director for Western and Central Africa.
"We need all partners and donors to step forward to prevent any more children from dying. No-one can take on a crisis of this scale alone."
Mr Fontaine said he had seen destroyed towns accommodating displaced people and thousands of frail children in desperate need of help.
"There are two million people we are still not able to reach in Borno state, which means that the true scope of this crisis has yet to be revealed to the world," he added.
"There are organisations on the ground doing great work, but none of us are able to work at the scale and quality that we need. We must all scale up."
MSF said in June that a "catastrophic humanitarian emergency" was unfolding at one camp in Bama, Borno state, where 24,000 people had taken refuge.
Many inhabitants were traumatised and one in five children was suffering from acute malnutrition, it said.
Town divided by Boko Haram legacy
On patrol against Boko Haram
Who are Boko Haram?
Almost a quarter of a million children in parts of Nigeria's Borno state formerly controlled by Boko Haram are suffering from severe malnutrition, the UN children's agency says.