The incident took place on Thursday night in the outskirts of the eastern town of Montbeliard.
“It has been confirmed that one of the men tried to present a health pass that did not match his identity,” the public prosecutor for the area, Ariane Combarel, told AFP.
READ ALSO: EXPLAINED: How the French health pass works
The pair then left the scene only to return a short while later in a car, from which several shots were fired in the direction of the club, she added.
A man who was enjoying a night out at the club sustained gunshot wounds to the knee, according to regional media.
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Combarel said he had required surgery and had been written off work for six weeks.
Since July, people in France have been required to present a Covid-19 pass in order to enter public venues such as restaurants, nightclubs, gyms or cinemas.
The pass, available in paper form or as a QR code on a smartphone, proves the person has been either vaccinated against Covid, recently tested negative for the virus or already had Covid and recovered from it.
Announced by President Emmanuel Macron in July, it prompted millions of people to get the jabs after holding out for months, giving France one of the world’s highest vaccination rates.
But the pass has also drawn controversy, with thousands of people attending weekly protests in cities across France against what they call Macron’s establishment of a health “dictatorship”.
A number of people have attempted to circumvent the rules by buying fake Covid passes on social media or using one belonging to a friend in the hope that they are not asked to produce ID.