No one was injured in the shooting, which occurred at night while the shop in the southern town of Popriano was closed, according to reports.
The shop that stands in the town centre was hit "by fire from heavy weaponry", the local prosecutor Eric Bouillard said. According to I-Tele there were around 30 bullet holes in the in the shop front.
The prosecutor believes an assault rifle was likely used in the attack and added the Muslim butcher who owned the shop had "no history" to explain why he was attacked.
There were also reports that a kebab outlet nearby was also hit by the gunfire.
Police have no indication who was behind the shooting, but it comes after communal tensions on the island between north African immigrants and locals flared in recent months.
The island was rocked by anti-Arab riots over Christmas after firefighters and police officers were ambushed and attacked on Christmas in a neighbourhood mostly home to north African immigrants.
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Demonstrators shouting slogans such as "This is our home!" and "Arabs get out", vandalised a Muslim prayer hall and set fire to books including copies of the Koran.
Six people have been charged in connection with that unrest.