Al Jazeera has demanded the release of a top staff member who was detained when Egyptian security officials raided the Mubasher Misr channel, shortly after Mohamed Morsi was ousted as president.
Three other television channels, all deemed to be pro-Morsi by Egyptian authorities, were also shut down on Wednesday in a move condemned by rights groups and journalists.
Mubasher Misr's managing director Ayman Gaballah remains in custody. Four other staff members have been released.
Global press news agency Associated Press Television News (APTN) was told not to provide Al Jazeera with any footage of the demonstrations in Egypt or any filming equipment, while the Cairo News Company was warned against providing broadcasting equipment.
Al Jazeera Media Network's acting Director General Mostafa Souag condemned the actions, saying "regardless of political views, the Egyptian people expect media freedoms to be respected and upheld."
"Media offices should not be subject to raids and intimidation. Journalists should not be detained for doing their jobs."
Al Jazeera Mubasher Misr, was prevented from broadcasting from a pro-Morsi rally in northern Cairo and its crew there was also detained.
Authorities claim it was operating without a proper licence, despite having been a live channel for several years.
Al Jazeera's Egyptian station began broadcasting after the 2011 revolution that topped President Hosni Mubarak and has been accused by critics of being sympathetic to Morsi's Muslim Brotherhood.
Egypt's military-led authorities also shut down a station operated by the Muslim Brotherhood after former President Mohamed Morsi was toppled.
Muslim Brotherhood-owned Egypt25 was forced off air and its managers arrested shortly after General Abdel Fattah al-Sisi, head of Egypt's armed forces, announced a plan for a new political transition, the state news agency MENA reported.
The authorities also shut down two other Islamist-run stations, Al-Hafiz and Al-Nas, security sources said.
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Both are affiliated to the strict Salafi Islamist movement.
"We are concerned by reports that authorities are shutting down television coverage based on political perspective," said Sherif Mansour of the New York-based Committee to Protect Journalists.
"We urge the military not to deprive Egyptians of information sources at this important juncture."
In a statement, the Brotherhood said the shutdowns were a return to the "repressive" policies of Egypt's "dark ... ages."
The London-based Amnesty International called the shutdowns a "blow to freedom of expression."
Speaking to Al Jazeera English, National Salvation Front spokesman Khaled Dawoud defended the move.
"I hope this is an exceptional measure that will last only for a few days," he said
"When you have a critical time of change like this and you have some other people who are trying to incite supporters to go and fight I don't think it is useful to have these channels working at these critical hours."