The Berlin-Brandenburg state laboratory has discovered bird flu pathogens in two birds in the Mitte and Treptow-Köpenick districts of Germany's capital, according to the Berliner Morgenpost.
This follows news over the past couple of weeks that the virus has been identified in several other German states and other European countries.
There is also a suspicion swans have been affected in Berlin's Landwehr Canal, which runs parallel to the River Spree in Berlin, but a final confirmation of that is still pending.
A dead seagull in the Brandenburg town of Werder near Potsdam was also discovered to have had bird flu, the state Consumer Protection agency disclosed on Friday.
The authorities swiftly set up a restricted area and a monitoring area around that location, and introduced restrictions on poultry owners.
Ducks, geese and chickens are not allowed to leave the restricted area for 21 days and the monitoring area for 15 days.
Existing stocks are then to be methodically checked, and cats and dogs prevented from roaming.
Brandenburg's Consumer Protection minister has imposed a quarantine on birds across the whole state.
This applies not only to commercial farmers but also hobby poultry owners, according to an agency spokesperson. The quarantines must be secure, and protective clothing worn, which must be disinfected on exit.
The state of Hamburg also implemented new rules on Sunday requiring dogs to be kept on leashes, and restricting the freedom of movement of cats, due to the spread of the highly contagious pathogen.