Those children "are not accessing basic health services, including vaccination against measles and polio", Martin Mogwanja, deputy executive director for operations at the UN children's fund (UNICEF), told reporters after a four-day visit to Sudan.
The youngsters are in rebel-held parts of the two states, where the Sudan People's Liberation Movement-North began an uprising in 2011 fuelled by complaints of political and economic neglect.
"It is not right for the different forces in conflict in those areas to hold these children as hostage, to hold their future as a hostage for the completion of a political process," Mogwanja said.
But the warring parties would still not let aid workers in, and UN humanitarian operations director John Ging earlier blamed a "filibuster" by both the government and rebels.
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If the campaign were to go ahead, it would be the first aid access into SPLM-N areas from within Sudan since 2011.
A broader internationally-backed plan to get food and other assistance to the rebel zone fell through more than a year ago despite months of talks with rebels and the government.
In April, the first peace talks in almost two years between the rebels and government stalled over the issue of humanitarian access.
The UN Security Council has stressed the need for a political solution to the conflict.
Sudanese authorities have severely restricted access to the warzones for aid workers, journalists and foreign diplomats.
Mogwanja said that in many cases UNICEF is not able to be present in Sudan's conflict areas, and he did not know how many children have been killed because of the war in South Kordofan and Blue Nile.