The order came yesterday after Saturday's editions of privately owned Al-Dustour daily featured a long front-page article warning of a Brotherhood emirate seizing Egypt and calling on Egyptians to join ranks with the military to oppose Islamists, state-run news agency MENA reported.
Editions of daily were seized and a probe has been launched after several individuals filed lawsuits accusing it of "fueling sedition" and "harming the president through phrases and wording punishable by law," it said.
Though it was not clear whether the paper was barred from publishing completely. However, the Al-Masry Al-Youm newspaper said that authorities have removed al-Dustour from newsstands.
Gamal Fahmy, a member of the journalists' syndicate, told Al-Dostour that the investigation was part of a Muslim Brotherhood scheme to limit press freedoms, local media said.
Other press freedom advocates also condemned the raid, saying the Brotherhood was moving to silence its critics.
The tabloid Al-Dustour, owned by a Christian businessman, has been known to criticise Morsi and the Muslim Brotherhood while showing strong support for the military council.
Earlier, a TV network was shut down due to the charges that it suggested the killing of the Morsi.