The first 150 cows arrived in the dark at 4 am on Saturday morning at the "Ferme des 1000 vaches" at Drucat in Picardie.
Opponents of the "factory farm" have been on site since Friday and are blocking access to trucks but not to the staff.
"If on Monday night, the farm construction magnate Michel Ramery doesn't agree to reduce to 500 the number of cows in the factory, we will set up a complete blockade of the site", said doctor Michel Kfoury, president of the Novissen protest group.
Opponents denounce the factory farm as a symbol of industrial agriculture which is ruining small farmers' livelihoods, is environmentally unfriendly and does not respect animal welfare.
Operation permits delivered in February 2013 authorize only a 500-cow unit so far, although the barn can house over 1,000 dairy cows.
The agriculture minister, Stéphane Le Foll embarrassed by the opening of the farm said on Sunday that he "didn't support " the factory farm but it "follows the rules".
In similar vein the ecology minister Segolène Royal said in July that farms like "Les Mille Vaches are not our economic model nor are they ecological. It is not our energy strategy".
A farmers union, the Confédération Paysanne, an active opponent of the project filed a suit on Monday alleging that the farm owner Ramery benefited from special treatments.
The Green party EELV also deplores that all appeals were not all fully examined.