About three quarters of the staff at the NIH, which operates the largest research hospital in the world, has been placed on unpaid leave indefinitely.
While the NIH Clinical Center is continuing to treat patients, it is operating at "roughly 90 per cent of normal patient load," said an agency memo.
"NIH would not admit new patients (unless deemed medically necessary by the NIH Director), or initiate new protocols," during a funding hiatus, the memo said.
About 10 of those children have cancer, he added.
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There are some 1,400 clinical trials ongoing at the NIH center, and four new ones ready to start next week will have to be postponed until the government resumes work, he said.
"Just to be clear, we aren't turning patients away permanently -- we would be delaying their admission, since we are not enrolling new patients at this time," spokesman John Burklow said in an email.
The Clinical Center is a place where patients are admitted "only when standard medical treatments have failed, and other treatment options are not available. As a result, they have no other alternatives," the memo said.
Some 800,000 federal workers across the US capital region and beyond have been told to stay home from work without pay, in the first US government shutdown in 17 years.
The shutdown came after Democrats refused to give in to Republican lawmakers' demands for a rollback of President Barack Obama's healthcare reform law, which Congress passed in 2010 and was subsequently upheld by the Supreme Court.