Cannes' mayor David Lisnard signed off on the ruling that "access to beaches and for swimming is banned to anyone who does not have (bathing apparel) which respects good customs and secularism," which is a founding principle of the French republic.
SOS Racisme attacked what it said was the mayor's "strategy of tension".
An umbrella organisation of groups against Islamophobia, the CCIF, said it was "deeply worried" about the ban, which it viewed as "a new attack on the most basic principles of law".
The ban also came under fire from the Socialist Party, who are in opposition to the centre-right Republicans who control Cannes. The local Socialist branch said the burkini ban was an attempt at grabbing headlines which would "play into the hands of religious fundamentalists".
Thierry Migoule, head of municipal services in Cannes, sought to clarify the intent of the burqini ban, which is in place until August 31.
"We are not talking about banning the wearing of religious symbols on the beach... But ostentatious clothing which refers to an allegiance to terrorist movements which are at war with us," he said.
On July 14 the nearby Riviera city of Nice was the target of an attack claimed by IS which killed 85 people, when a truck ploughed into crowds celebrating Bastille Day.
On July 26, a priest was killed in his church in northwestern France by two attackers who had proclaimed their allegiance to Islamic State.
Islamic dress is a hot-button issue in France, where the full-face veil is banned in public places. But there is no ban on wearing religious symbols or clothing.
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