Animal rights groups had proposed the move, saying that without lawyers to argue the animals' case, many instances of cruelty were going unpunished.
But the measure was rejected by around 70% of voters in a referendum.
Opponents had argued that Switzerland did not need more legislation. The government had opposed the idea.
Voters were almost certainly swayed by worries about how much such a system might cost taxpayers, and by objections from Switzerland's farmers already struggling with reduced subsidies and falling milk prices.
Switzerland already has some of the strictest animal welfare legislation in the world.
Pigs, budgies, goldfish and other social animals cannot be kept alone; horses and cows must have regular exercise outside in summer and winter; and dog owners have to take training courses to learn how to care for their pets.