Sudan coup: Armed forces fire on anti-coup protesters
"Military forces have fired live bullets on protesters rejecting the military coup outside the army headquarters," the ministry said in a statement on Facebook.
At least 12 people were injured in clashes on Monday, reported Reuters citing a doctors committee's Facebook page.
The violence erupted after Sudanese security officials detained civilian leaders, including Sudan's PM Abdallah Hamdok.
The PM's office called on protesters to take to the streets after civilian leaders were taken into custody in what the information ministry called a "coup".
"We call on the Sudanese people to protest using all peaceful means possible... to take back their revolution from the thieves," Hamdok's office said in a statement.
The "coup" follows weeks of tensions between the military and civilian figures sharing power since the ousting of autocrat Omar al-Bashir.
Internet services have been cut across the country. The main roads and bridges connecting with Khartoum were closed down.
Soldiers stormed the headquarters of Sudan's state broadcaster in the capital's twin city of Omdurman, as patriotic songs were aired on television.
The UN, EU and US have expressed grave concerns about the unfolding situation in Sudan.
Volker Perthes, UN special representative to Sudan, said: "I am deeply concerned about reports of an ongoing coup and attempts to undermine Sudan's political transition. The reported detentions of the Prime Minister, government officials, and politicians are unacceptable."