Al Jazeera said Egyptian security forces have arrested three of its journalists after the Interior Ministry accused the Qatar-based television channel of broadcasting illegally from a hotel suite together with a member of the Muslim Brotherhood.
Al Jazeera's offices in Cairo have been closed since 3 July when they were raided by security forces hours after the army ousted the Brotherhood's Mohammed Mursi from the presidency.
"State security received information that a member of the (Brotherhood) used two suites in a Cairo hotel to hold meetings with other members of the organisation and turned the suites into a press centre," the Interior Ministry said.
"(They) made live broadcasts of news that harms homeland security, spreading rumours and false news to Qatar's Al Jazeera channel without permits."
A member of the Brotherhood and an Australian journalist who works for Al Jazeera were arrested and equipment was seized, including broadcast transmitters, the Interior Ministry said in a statement.
Al Jazeera said three of its journalists had been arrested; a correspondent, a producer and a cameraman.
Qatar was a strong financial backer of the Brotherhood's rule.
Its relationship with Cairo has deteriorated in recent months, as it vehemently opposes the army's overthrow of Mr Mursi and the crackdown on his movement that has followed.
Since Mr Mursi's ouster, Egypt has faced some of its worst violence in decades, which the government has blamed on Islamic militants.
It declared the Brotherhood a terrorist group last week and has arrested thousands of its members, including Mr Mursi.
US Defence Secretary Chuck Hagel expressed concern about recent developments in Egypt in a call yesterday to Egyptian army chief General Abdel Fattah al-Sisi, discussing the "balance between security and freedom".
The New York-based Committee to Protect Journalists (CPJ) has classified Egypt alongside Syria and Iraq as one of the most dangerous countries for journalists to operate in.
"Amid stark political polarisation and related street violence, things deteriorated dramatically for journalists in Egypt, where six journalists were killed for their work in 2013," the CPJ said.
Egypt is pushing through a political transition that could lead to presidential and parliamentary elections next year.
A constitutional referendum is due to take place in mid-January.