The United Nations said in a statement it was issuing the call after at least 50 men in civilian clothes raided the Cairo offices of the Egyptian Center for Economic and Social Rights Wednesday.
The men were later identified as police officers, the statement said.
The U.N. Office of the High Commissioner for Human Rights said six employees of the non-governmental organization were arrested and allegedly beaten. Laptops, files and documents were seized.
"The raiding of a human rights NGO and the arrest of six of its members in Cairo on Wednesday night marks a worrying escalation in the harassment and intimidation of civil society in Egypt," said Ravina Shamdasani, an OHCHR spokeswoman.
She said five of the employees were released after nine hours, but a sixth worker remained in detention.
"We call on Egyptian authorities to immediately release all individuals who have been detained in relation to their work as human rights defenders," Shamdasani added. "Intimidation of political opponents, activists and human rights defenders for peaceful exercise of their fundamental rights to freedom of expression and association must be halted."
Protests last summer in which dozens of people were killed or injured led the army to depose President Mohamed Morsi. Since then, the constitution has been suspended and an interim government established.