Mally the Monkey was seized by German customs March 28 when teen singer Justin Bieber failed to produce required vaccination and import papers for the animal after landing in Munich for a European tour.
He had until midnight on Friday to produce those documents.
Customs spokesman Thomas Meister said after offices opened following a holiday weekend that officials had received no documents. He said the customs authority issued an order later on Tuesday formally transferring ownership of the animal to the German state.
Bieber, 19, has six weeks to contest the decision if he wants to do so. Germany's Federal Agency for Nature Conservation said the monkey would be sent to a zoo somewhere in Germany, but officials declined to say exactly where to avoid security problems.
Mally, a capuchin monkey, has been cared for at Munich's animal shelter since being taken into quarantine. The shelter's manager said Mally, who is now 20 weeks old, has fared well and gained weight in its care.
The shelter has criticised Bieber for keeping such a young monkey as a pet, saying it should not have been taken away from its mother until it was a year old. Experts said capuchin monkeys also need to be kept in groups as they are very sociable animals.
German authorities now hope to reclaim the cost of Mally's upkeep at the Munich shelter over the past two months, including care, food and vet visits.
Mr Meister said a bill would be prepared and sent to Bieber. He put the cost at several thousand euros but said authorities would not detail the specific amount.