Thirteen non-governmental organisations said on Wednesday that in recent weeks the Egyptian authorities had questioned several human rights workers, barred them from travel and also attempted to freeze their assets.
"More than 47,000 NGOs are working in Egypt, including nearly 100 foreign NGOs who are operating freely in many fields," the foreign ministry said in a statement.
Fresh criticisms erupted after a probe was launched against two prominent Egyptian human rights defenders, Gamal Eid and Hossam Bahgat, for receiving foreign funds.
On Thursday, a Cairo court postponed until April 20 a hearing to determine whether to freeze their assets and ban them from travelling abroad.
Under Egyptian law, members of rights groups operating without registration or accepting foreign funding without government permission could be jailed for life, which in Egypt amounts to 25 years.
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The foreign ministry said in 2015 the government "rejected approximately seven percent of foreign funding to be provided to civil society organisations," adding other groups received an estimated $100 million legally.
This made it "impossible to claim that there is a stifling of the work of civil society organisations in Egypt," it said in a statement.
Since the 2013 ouster of Islamist president Mohamed Morsi, the authorities have led a crackdown on all forms of dissent -- not just Morsi's supporters but also liberal and rights activists.
Rights groups have regularly accused Egypt's security services of carrying out illegal detentions, forced disappearances of activists and torture of detainees.
"NGOs who have played a valuable role in documenting violations and supporting victims will see their activities completely crippled if this continues," UN High Commissioner for Human Rights Zeid Ra'ad Al Hussein said this week.
"This will stifle the voices of those who advocate for victims," he said in a statement.