An employee at the visa section had reported breathing difficulties and a metallic taste in her mouth after opening a passport handed to her by a male visitor, believed to be Albanian, police said.
The alarm came amid attacks on US embassy and consulate buildings across the Middle East.
The Berlin consulate is in the southwest of the city, separate from the main embassy building in central Berlin.
Demonstrators attacked the US embassies in Yemen and Egypt on Thursday in protest over a film they consider blasphemous to Islam, and American warships headed to Libya after the death of the US ambassador there in related violence earlier in the week.
Islamist gunmen had staged a military-style assault on the US consulate and a safe house refuge in Benghazi, eastern Libya.
The US ambassador Christopher Stevens and three other Americans died in the assault, carried out with guns, mortars and grenades.