Yesterday's raid on Al-Hurriya Wal Adala's offices came a day after a Cairo court banned the Brotherhood and ordered its assets seized, delivering a vital blow to the movement of deposed president Mohamed Morsi.
The moves by Egypt's army-backed authorities are part of a sustained campaign against the Islamist movement since Morsi was ousted by the army on July 3 after mass street protests against his year-long rule.
"The forces of the military coup in Egypt closed the headquarters of Al-Hurriya Wal Adala newspaper which is the mouthpiece of the party," said Ikhwanonline, the Brotherhood website.
"We, the journalists of Al-Hurriya Wal Adala, condemn the closure of the newspaper's headquarters by security forces of the coup who took all documents, equipment and other materials" from the premises, the statement said.
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The journalists said that since July 3 "we have been working under pressure and intimidation from the security forces and thugs".
The website said that "there was no warning, no legal decision against our journal," adding that since June 28 no journalists had been working in the actual headquarters.
The raid ratchets up an intensifying crackdown.
More than 100 policemen have also been killed in clashes with Morsi's supporters since his overthrow.
Meanwhile, the Brotherhood has until October 2 to file an appeal against Monday's court decision, failing which the authorities are expected to proceed with implementing its rulings.