Fighters "kicked out all the technicians from the lab... which is completely under the control of one of the fighting parties as a military base," said Nima Saeed Abid, the WHO's representative in Sudan.
He did not say which of the fighting parties had taken over the laboratory.
Abid said he had received a call from the head of the national lab in Khartoum on Monday, a day before a US-brokered 72-hour ceasefire between Sudan's warring generals officially came into effect after 10 days of urban combat.
"There is a huge biological risk associated with the occupation of the central public health lab," said Abid.
He pointed out that the lab held so-called isolates, or samples, of a range of deadly diseases, including measles, polio and cholera.
The UN health agency also said there had been 14 attacks on healthcare facilities or personnel during the fighting, leaving eight healthcare workers dead and two injured.
And it warned that "depleting stocks of blood bags risk spoiling due to lack of power."
"In addition to chemical hazards, bio-risk hazards are also very high due to lack of functioning generators," Abid said.
The Sudanese health ministry has put the number of deaths so far at 459, with a further 4,072 wounded, the WHO said Tuesday, adding it had not been able to verify that number.
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