The clashes broke out on Thursday in the Kouri Bougoudi area of the Tibesti border region, the Chadian Convention for the Defense of Human Rights (CTDDH) said in a statement.
At least 30 gold miners were killed and more than 200 wounded, it said.
Abdul Aziz Youssouf Mustapha, a Chadian with the International Federation of Human Rights (FIDH), said the fighters attacked all "non-Arabs" who had come to Kouri Bougoudi in search of gold, Presstv reported.
All miners were forced off the gold-mining area on Saturday, he said.
A military source confirmed that there had been fighting but did not give further details.
Many of the miners hailed from the Ouaddai region in central-eastern Chad. Sources among the Ouaddai community also confirmed there had been clashes in Kouri Bougoudi.
Kouri Bougoudi has been a theatre of violence since discoveries of gold were made there in 2012 and 2013.
Miners have rushed in from around Chad and abroad, leading to friction over access to lucrative sites.
The CTDDH accuses the government of orchestrating a takeover of the area by using Arab fighters.
The government has given authorization to several mining companies to exploit the deposits.
In August, it carried out a military operation in the far north aimed at "clearing out" illegal miners and stopping cross-border incursions from Chadian rebels holed up in Libya.