The move against Zaman came days after Turkey’s Constitutional Court ordered the release from detention of two Turkish journalists charged with revealing state secrets.
Police entered the building in Istanbul late on Friday, firing tear gas at protesters, who had gathered outside.
Zaman is closely linked to the Hizmet movement of influential US-based cleric, Fethullah Gulen.
Turkey said that Hizmet is a “terrorist” group aiming to overthrow President Recep Erdogan’s government.
The government in Ankara has come under increasing international criticism over its treatment of journalists.
Earlier, Zaman said Turkey was going through its “darkest and gloomiest days in terms of freedom of the press.”
The newspaper’s website was still functioning on Saturday, but did not carry news of the raid.
The US State Department described the takeover as “the latest in a series of troubling judicial and law enforcement actions taken by the Turkish government”.
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