The Central Narcotics Office (OCS) in a Facebook posting said there had been "vigorous" raids by its agents in Bamako, culminating in "about 50 individuals in prison and a large amount of seized material."
It published photos of young men and women being taken away in the back of pickup trucks and a picture of a pile of water pipes.
"The grace period given by the authorities for importers, distributors, sellers and consumers of shisha in Mali is over," the OCS said.
The country's anti-drug agency says it has carried out dozens of arrests in the capital Bamako and seized water pipes after the six-month moratorium expired.
Bars where small groups of smokers -- primarily young men -- hang out to chat and puff on hookahs have flourished in Bamako in recent years.
But their days became numbered when the junta-dominated government on August 15 announced a surprise ban.
It warned that shisha smokers would be liable to a prison term of one to 10 days and a fine of 300 to 10,000 CFA francs ($0.45 to $15).
The ban has divided opinion in Mali.
The country is overwhelmingly Muslim, and interpretations of Islam are generally unfavourable to cigarettes and to shisha.
But it is also a secular nation that tolerates alcohol, even if consumption is limited to certain public places and most shops and restaurants do not serve it.
Shishas, or hookahs, typically burn tobacco flavored with fruit to provide a sweetened taste. The smoke is inhaled in through a long rubber tube, passing through water to cool it down. "Shisha" is also the term sometimes used for the tobacco product.
A working group of the World Health Organization (WHO) warned in 2017 about the danger of shisha smoking.
The practice is up to 10 times more harmful than cigarettes but is not targeted by the same awareness campaigns as with tobacco, it said.