Brahim told a press conference that the confrontation between the Sudanese might create new waves of refugees and added that maintaining security would become difficult.
Chad's government closed its border with Sudan on Saturday and called for calm amid an apparent coup attempt in Khartoum by Sudan's main paramilitary group.
The West African country's defense minister said that the country had hosted more than 400,000 Sudanese refugees in the past.
"Today, thousands of refugees are crossing our border to seek protection. We have no choice but to welcome and protect them," Brahim said.
(Reporting by Mahamat Ramadane; Writing by Anait Miridzhanian; Editing by James Macharia Chege)
