The raids involving 130 officers including members of a tactical response team were part of an investigation against four people on suspicion of membership in IS or preparing an attack.
Berlin prosecutors said two of the suspects are believed to have left Berlin in November 2016 to join IS, which was mainly active in Syria and Iraq at the time.
A third is suspected to have undergone military training with the group. All three are still believed to be in IS-held territory, prosecutors said.
They declined to comment immediately on a report by Berlin daily BZ that the suspects have been linked to Anis Amri, the Tunisian who killed 12 people in a truck rampage at a Christmas market last year. Amri was shot dead by Italian police days later. The attack was claimed by IS.
Separately, prosecutors in the state of Lower Saxony said today that the police arrested two 21-year-old Palestinian men who had spread jihadi material and threatened online to commit attacks "in order to create a climate of insecurity and fear."
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