Authorities in the Boucle du Mouhoun region said they were shutting 43 makeshift mines for security reasons.
Regional governor Babo Pierre Bassinga said the sites would be closed until further notice in a decree published on Wednesday but dated February 27.
Violators face criminal charges.
A local security source told AFP the move aimed at curbing trafficking in explosives and cutting off an income source for armed groups, which extort money from the miners.
Gold has overtaken cotton to become Burkina Faso's main export, with legal mines producing around 70 tonnes per year.
But there is also a flourishing informal sector, employing more than a million people and producing around 10 tons per year, according to official estimates.
The authorities are struggling to regulate unauthorized mining, where deadly accidents are common.
The poor West African nation has also been plagued by deadly insurgent attacks since 2015, leaving more than 10,000 people dead, according to NGO estimates, and displacing around two million.