Corsica's Prefect Christophe Mirmand met representatives of the protesters in the regional capital Ajaccio on Saturday and asked them to stop "these movements and this demonstration that gives such a disastrous image of Corsica".
He later announced that he would ban protests in and around the Jardins de l'Empereur estate where the violence took place.
The members of the delegation told reporters they were satisfied with Mirmand's promise to post police in all areas of Ajaccio.
Riot police and gendarmes stopped a crowd of about 300 entering the estate on Sunday.
There was a heavy police presence on the estate when about 100 protesters arrived mid-afternoon Saturday before going to neighbouring districts.
One man smashed the glass doors of three apartment buildings but no other incidents were reported.
The estate has a bad reputation on an island with a history of organised crime but a low level of street-level criminality and the planned assault on firefighters by a small group angered many local people, some of whom are volunteers in a service that is called on to fight forest fires every summer.
Corsican nationalist youth groups have denied reports that they were involved in the protest that led to the attack on the prayer room, with the largest, Ghjuventu independista, joining politicians who have condemned all of the violence.
Following Saturday's statements by Prime Minister Manuel Valls and Interior Minister Bernard Cazeneuve, right-wing former prime minister Alain Juppé called for "authority and firmness".
But the far-right Front National declared that there was a risk of "citizens" taking matters into their own hands when they have "the legitimate feeling that the government no longer enforces republican order".
Hard-left former presidential candidate Jean-Luc Mélenchon linked the protests to the "ethnicist inebriation" of the Corsican nationalists and Corsica's "exacerbated nationalism and culture of violence".
His Communist Party allies declared it "incomprehensible that people demonstrate using racist and xenophobic phrases in Ajaccio while during the Cop21 [climate conference] environmental activists were arrested and some placed under house arrest for supposed threats to public order".