David Nabarro, head of the World Health Organisation (WHO) health crisis action group in Geneva, said on Friday the monthly death rate in Darfur was about 10,000, blaming malnutrition and disease.
He said the figure of 70,000 did not take into account deaths from violence.
But Foreign Minister Mustafa Uthman Ismail said on Saturday the information was not correct and that, when the Sudanese Government asked the WHO's Khartoum office for details, employees said the information had not come from them.
"When we checked with the office of the WHO here, they told us they have no information. This information never came from them," Ismail said. "They are the ones who are on the ground here. They know what is going on."
Ismail said the government will investigate whether the WHO was under pressure to issue false figures. "We are not going to leave these issues until they are tackled," he said.
After years of skirmishes between nomads and farmers over scarce resources in Darfur, rebels took up arms, accusing Khartoum of neglect and of using the Janjawid to fight rebels.
Khartoum has denied any links to the Janjawid, calling them bandits.
Rebels are accused of exploiting
the Darfur situation for power
The Janjawid had agreed in previous negotiations to be garrisoned while rebels in the south refused and constantly walked out of African Union-brokered peace talks.
The rebels are accused by Sudan of seeking power and control by exploiting the Darfur situation.
The United States calls the violence genocide while the EU has said it cannot be referred to as "genocide".
The UN Security Council has threatened Sudan with possible sanctions over the Darfur crisis.
The world body also says 1.5 million people have been displaced due to the conflict.