The medics said "live rounds" were fired at protesters in Omdurman and parts of Khartoum.
More than 100 people were also wounded on Saturday, some suffering breathing difficulties due to tear gas, the committee added.
Sudan's interior ministry denied that live rounds were fired at protesters on Saturday, saying the reported killings were "inaccurate".
"Groups of protesters ... attacked the police, as well as vital sites, which prompted the police to fire tear gas," a statement said.
An AFP correspondent said tear gas was fired at other protests on the eastern banks of the Nile in Khartoum.
Security forces had deployed in large numbers and blocked bridges to Khartoum.
Tens of thousands turned out across the country for Saturday's demonstrations, which came almost a week after Monday's power grab, when the military dissolved the government, declared a state of emergency and detained Sudan's civilian leadership.
The move sparked a chorus of international condemnation, with world powers demanding a swift return to civilian rule.
"No, no to military rule," protesters carrying Sudanese flags chanted in Khartoum.
Organisers had aimed to stage mass protests similar to those that led to the toppling of autocrat Omar al-Bashir in 2019.
'Don't back down'
As night fell, many protests in Khartoum and Omdurman thinned out, AFP correspondents said.
Demonstrations took place across the country during the day, from Khartoum to the eastern regions of Gedaref and Kassala and the Red Sea city of Port Sudan, as well as central North Kordofan state and southern White Nile state, witnesses and AFP correspondents said.
"We want civilian rule... It has to be civilian 100 per cent," said Hashim al-Tayib, a protester in southern Khartoum.
From autocracy to military coup: A timeline of power in Sudan since 2019
Sudan had been led since August 2019 by a civilian-military council which was supposed to last three years and lead to full civilian rule.
The arrangement came under increasing strain prior to the coup, which analysts said aimed to maintain the army's traditional control over the north-east African country.
Protesters held posters of Prime Minister Abdalla Hamdok, ousted by the military and effectively held under house arrest, with slogans saying, "Don't back down".
"Though I have reservations on the performance of Hamdok's government, there is no substitute for it," said protester Hagar Youssef.
Protesters in east Khartoum burned tyres and held posters reading, "It's impossible to go back", while in the city's southern district, banners expressed concern that the country might return to Washington's state sponsors of terrorism list.
That designation, accompanied by years of crippling sanctions, was lifted only last December, opening the way to debt relief and renewed largesse from the International Monetary Fund and World Bank.
After Monday's coup, the World Bank suspended aid to Sudan in a heavy blow to a country already mired in a dire economic crisis that began under Mr Bashir.
The World Bank has suspended operations in Sudan following the military coup
Other protesters called for "freedom to the members of cabinet" who have been detained since the putsch.
Several pro-democracy activists have also been arrested following the takeover led by General Abdel Fattah al-Burhan, Sudan's de facto leader since the ouster of Mr Bashir which came at the cost of more than 250 lives.
Warnings on violence
Officials from the United Nations, the US and Britain have urged security forces to refrain from violence and show "restraint".
"The security services and their leaders will bear responsibility for any violence towards any protesters," said Robert Fairweather, Britain's special envoy for Sudan and South Sudan.
Saudi Foreign Minister Prince Faisal bin Farhan said on Saturday that Sudan's security was "of paramount importance" to the Gulf kingdom and called for "a Sudanese dialogue that brings together all parties".
Before the protests began, Sudan's information ministry, which backs a civilian government, warned that coup authorities were planning to engineer "instances of destruction to justify its excessive violence".
Shops have largely been shuttered, and government employees have refused to work as part of a campaign of civil disobedience.
Mr Burhan, a senior general under Mr Bashir's three decades of iron-fisted rule, has insisted the military takeover "was not a coup" but only meant to "rectify the course of the Sudanese transition".
Sudan has enjoyed only rare democratic interludes since independence in 1956 and spent decades riven by civil war. SBS