"So far, we have counted four deaths as a result of the forces' use of live bullets," the ministry said on its Facebook account, Xinhua reported.
Earlier, the Central Committee of Sudanese Doctors (CCSD), a non-governmental organization, said three people were killed "in the processions in Omdurman by the bullets from the coup forces and the their (allied) militias."
"The authority is practising the most heinous violations against our people, and the chases continue in the neighborhoods with live bullets being fired," the CCSD said on its Facebook account.
So far, no statement has been issued by the Sudanese government on Thursday's demonstrations.
Omdurman is the most populated city in Sudan and Khartoum State, lying on the western bank of the Nile river, opposite the capital Khartoum.
According to unofficial statistics, 52 people have been killed in the protests after the general commander of the Sudanese army declared a state of emergency on Oct. 25 and dissolved the government.
Mass protests were staged in Khartoum and other cities on Thursday to demand civilian rule, while the internet service on mobile phones was interrupted.
RHM/PR
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