Authorities also extended the detentions of three others taken in for questioning after the shops were searched by the drugs squad on Wednesday.
The two so-called "coffee shops" -- one of which had queues out the door in recent weeks -- are among dozens which have sprung up across France in recent months.
They claim to be legally offering marijuana buds, oils and other products obtained from plants with less than the French limit of 0.2 percent of THC, the psychotropic compound that produces a high.
Instead the products contain cannabidiol, or CBD, a compound used for medical marijuana treatments and which is authorised in France.
Investigators suspect small traces of THC may nonetheless be present in the products, which would be illegal under French law.
Under a recent notice by the country's anti-drugs task force, marijuana buds and leaves remain illegal, whether they contain THC or not.
The government has announced plans to soften penalties for cannabis use, scrapping potential prison sentences for on-the-spot fines, but it remains opposed to legalising the drug.
A recent survey found 51 percent in favour of limited legalisation, reflecting a growing trend toward more relaxed rules in Europe and the United States.