Mally, a capuchin monkey, is temporarily in an animal refuge in the southern city of Munich where he was visited Tuesday by Germany's environment minister.
"Animals are not toys," Peter Altmaier said, warning against people having animals they are unable to care for.
Munich customs authority spokesman Thomas Meister said that Bieber "has not come forward" since the monkey was confiscated at the city's airport at the end of March when the teen heartthrob was unable to present the necessary documents for importing a live animal.
The pet was reportedly a birthday present from Bieber's record producer and accompanied him on a private jet to Munich while the 19-year-old toured Germany and Austria.
Authorities had said that the singer had four weeks to provide the required paperwork and claim his pet or else Mally would be kept permanently at an animal shelter.
Although that deadline passed on Friday night, they decided to wait until Tuesday morning before definitively holding the animal. Bieber has however six weeks to appeal.
According to the customs authority, the singer is expected to have to foot the bill, which may come to several thousand euros, for the monkey's upkeep since its arrival in Germany. Animal protection services could also fine the singer.
In the meantime, Mally will be housed in a "secret" place in Germany to shelter it from attention.
"It needs calm," the spokesman said, adding that after this quarantine period, it would have to re-adjust to living with other monkeys.