The law, passed almost unanimously last week by the country's Communist-controlled legislature, gives police wide-ranging powers over overseas charities and bans them from recruiting members or raising funds in the country.
At least 1,000 foreign NGOs are thought to operate in China, including development charities such as Save the Children, advocacy groups including Greenpeace, chambers of commerce and university centres.
Three UN human rights special rapporteurs said they feared the law's "excessively broad and vague provisions" and discretion given to authorities "can be wielded as tools to intimidate, and even suppress, dissenting views and opinions in the country".
China's foreign ministry spokesman Hong Lei told reporters Beijing "firmly opposed" the declaration, which was "utter interference in China's judicial sovereignty and domestic affairs".
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The law was intended to "protect the legitimate rights and interests of overseas NGOs", he said, insisting that the legislative process was transparent and outside inputs had been taken into account.
But the European Union delegation to China said Wednesday that its most important suggestions had gone unheeded.
The law gave the government "virtually unlimited authority to monitor and interfere with NGO affairs", it said.
Any groups committing actions deemed "separatist" or "subverting of state organs" will also be banned, as will those which "spread rumours".
The legislation comes as President Xi Jinping oversees a crackdown on civil society, which has seen scores of lawyers, academics and activists detained and dozens jailed.