The privately owned daily newspaper Al-Dostour is being investigated on charges of insulting President Mohamed Morsy, state-run MENA reported on Saturday.
Al-Dostour's website reported that early morning Saturday, security forces came to the paper's offices to confiscate some of its issues.
MENA reported that investigations into the newspaper had been opened after people accused the newspaper of "fueling sedition," and "harming the president through phrases and wording punishable by law."
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
Other press freedom advocates also condemned the raid, saying the Brotherhood was moving to silence its critics.
"What happened this morning is a new attempt to impose hegemony, domination and exclusion on those in conflict with the group," said Saeed Ziauddin Garhi, legal advisor for the Justice Center for Freedoms.
Earlier this week, Al-Faraeen Satellite TV channel, owned by the famous TV personality and former parliamentary candidate Tawfiq Okasha, was shut down, due to charges that the TV host incited viewers to attempt to assasinate Morsy.
Al-Dostour was also controversial under former President Hosni Mubarak; in 2010 the mogul publisher sacked Editor in Chief Ibrahim Eissa, an outspoken government dissident. Many claimed that the publisher had fired Eissa under direct pressure from the regime.