Egyptian police arrested Azza Soliman, who founded the Center for Egyptian Women's Legal Assistance, at her home and briefly detained her for questioning on allegations of taking foreign funds to "harm national interests," according to her lawyer.
"This is the latest manifestation of the progressive closing of space for the public exchange of views in Egypt," said UN spokesman Farhan Haq.
"The secretary-general underscores the important role that civil society and NGOs play in assisting governments to meet both developmental and civil objectives," he added.
The United Nations had raised concern about Cairo's decision in September to freeze the assets of several prominent rights activists and NGOs, which stoked fears of a crackdown on civil society.
Under Egyptian law, members of rights groups operating without registration or accepting foreign funding without government permission could face lengthy jail sentences.