"This is the first time that police have stormed the headquarters of the association," its head Yahiya Kallash told AFP, adding that journalists Amr Badr and Mahmud el-Sakka were arrested.
A judicial source said the pair had been wanted by the prosecution service for alleged incitement to protest in violation of the law.
Badr heads the website Babawet Yanayer which is opposed to President Abdel Fattah al-Sisi. Sakka works for the same organisation whose Arabic name means January Gate in a nod to the January 2011 uprising.
On Friday, Badr had written on his Facebook page that police had raided both his and Sakka's home.
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The following day Badr announced that the pair had started a sit-in in protest at the headquarters of the union.
Sakka had announced on Facebook plans to join an April protest against a decision by the government to hand over to Saudi Arabia two Red Sea islands.
According to rights group Amnesty International, Egyptian security forces arrested hundreds of people ahead of planned protests last month.
In July 2013, Sisi, then the army chief, overthrew Egypt's Islamist president Mohamed Morsi and began a deadly crackdown on his supporters.
Authorities have since banned all but police-approved rallies and overseen a crackdown that has left hundreds of Morsi supporters dead and thousands imprisoned.
Several secular and leftist activists who spearheaded the 2011 uprising against longtime strongman Hosni Mubarak have also been jailed.