The two individuals, aged 28 and 46, had been "in contact with the Islamist movement," police spokeswoman Patricia Braemer said.
The police gave no further details, other than to say no arms or explosives had been found and there was no indication that "an act of violence was planned for Berlin."
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The two arrests were made in Britz, where a neighbourhood was sealed off to let experts examine a suspicious object in a car that turned out to be harmless, police said earlier.
Local media reported officers had acted on a tip-off that an attack was being planned, as European police forces are on high alert following the bloody jihadist attacks in Paris on November 13.
A Germany-Netherlands football match in Hanover was called off last week at the last minute over fears of an assault.
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