Despite the breaches, the court found the European Commission failed to prove Finland had pursued a consistent policy of culling wolves "without evaluating conservation of the species or without providing a strict and adequate reason for an alternative solution".
Finland says it uses many different methods of reducing damage to livestock from wolves, but that in some cases it needs to allow culls.
"If we can prove that hunting can prevent damage, then permits can be issued," Finnish agriculture ministry official Sami Niemi told Reuters.
"The most important thing in the court ruling is that the current system based on granting permission is not against the EC Habitats Directive," the ministry said in a statement.