The Swedish Transport Agency made the decision after an operation on Saturday morning.
The ban on use means the ship, which is on the EU's sanctions list, is not allowed to travel further.
"It must not leave until the deficiencies we have identified are remedied. It is up to the shipping company to do so," says Mikael Andersson, press officer of the Swedish Transport Agency.
When the Sea Owl I was boarded, a preliminary investigation was opened into lack of seaworthiness, use of false documents, felony and other violations of maritime law. The ship's master, who is Russian, has been arrested.
This is the second time in a short period that a ship has been boarded off the coast of Skåne.
