The 19-year-old Canadian arrived at Munich Airport last Thursday.
Customs spokesman Thomas Meister said today that when the singer went through customs he did not have the documentation necessary to bring the capuchin monkey into the country - so the animal had to stay with authorities.
Bieber performed in Munich on Thursday night on the latest leg of his European tour. He is playing several concerts in Germany and Austria over the next week.
Bieber had a trying stay in London recently, first being booed by fans when he arrived late at a concert, then struggling with his breathing and fainting backstage at a show, and becoming involved in a fracas with a photographer outside his hotel.