Human rights activists accuse President Abdel Fattah al-Sisi of running an ultra-authoritarian regime that has violently suppressed all opposition since toppling Islamist president Mohamed Morsi in 2013.
On Sunday, police sparked media and opposition outrage by storming the journalists' union building in an unprecedented raid and arresting two reporters.
A day later, the authorities ordered the detention for 15 days of Amr Badr and Mahmud el-Sakka on allegations of incitement to protest.
Badr heads the website Babawet Yanayer which is opposed to Sisi.
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Sakka works for the same organisation whose Arabic name means January Gate in a nod to the January 2011 uprising that forced longtime strongman Hosni Mubarak to stand down.
"This year we mark World Press Freedom Day with Egypt down in all the international rankings," union chief Yahiya Kallash told a press conference ahead of a union general meeting due tomorrow.
"Instead of seeing the government take concrete measures to overcome this situation, we are surprised to see it escalating the war against journalism and journalists," he said.
He said "29 journalists are currently behind bars, some of whom have been in custody for nearly three years".
The union chief addressed an often rowdy press conference of some 200 journalists during which he was interrupted by chants against the police who controlled access to the building.
"Interior ministry thugs!" they chanted.