What began as a “mundane dispute between two individuals… degenerated”, Defence Minister Daoud Yaya Brahim told the AFP news agency.
The mountainous Kouri Bougoudi district near the Libyan border attracts miners from across Chad and its neighbours.
The clashes occurred last week but details are only emerging now.
Some groups have put the death toll higher than the authorities, and have blamed the security forces for a number of the deaths.
The government sent a mission to the affected area – about 1,000km (620 miles) northeast of the capital, N’Djamena – when news of violence first came through.
A large military contingent has restored calm to the area, Gen Brahim is quoted by AFP as saying.
He added that the clashes were between people from Mauritania and Libya.
But last week, Mahamat Nour Ibedou, the head of Chad’s National Human Rights Commission, said the soldiers who were sent to intervene “fired on people”, AFP quotes him as saying.
He, and an opposition leader, put the death toll at 200, but the authorities deny this and say they were not responsible, AFP reports.
All gold mining activities in Kouri Bougoudi have now been suspended.