The move came after hundreds of armed men attacked Masteri, a town largely inhabited by farmers from non-Arab minority groups, killing more than 60 people and wounding dozens.
Save the Children, which said five children were among the dead, announced the temporary closure of two health facilities and its field office in Masteri, cutting off “more than 14,000 children from life-saving health services”.
“The health facilities were the only two centres which provided health and nutrition services for children in the area,” it said.
The attack sparked panic in Masteri and nearby villages.
The United Nations humanitarian coordination office OCHA said around 10,000 people had fled towards the town of El-Geneina and another 1,000 had crossed the border into Chad.
Conflict struck Darfur in 2003 when ethnic minority rebels took up arms against then-president Omar al-Bashir, citing marginalisation and discrimination.
Khartoum responded with a scorched-earth campaign that left 300,000 people dead and displaced 2.5 million.
Violence in Darfur had eased since Bashir’s ouster by the army amid mass protests against his rule last year, and after an interim deal between the transitional government and rebel groups.
But recent weeks had seen a surge as long-displaced farmers returned to their land.
On Sunday, Prime Minister Abdalla Hamdok said security forces would be deployed to the arid western region to protect residents and allow the farming season to go ahead.
Arshad Malik, Save the Children’s Sudan director, called on Khartoum to investigate the killings and bring those responsible to justice.
“It is indefensible that children have been killed and wounded in the violence, and our thoughts go out to their families,” he said.
“If the centres are not reopened soon, children’s lives will be put at further risk. With already 1.1 million children facing hunger in Sudan, this conflict can only increase the number of children in need.”