Iranian Foreign Ministry spokesman Seyyed Abbas Mousavi condemned the measure as a "flagrant violation of Resolution 2231 and the Charter of the United Nations."
He said Iran was ready to "take legal action and act appropriately" if the move harms its nuclear rights.
The waivers were part of the landmark accord under which Iran agreed to limit its nuclear work in return for lifting economic sanctions.
They allowed European, Chinese, and Russian companies to work on the conversion of a heavy water reactor in Arak, a major industrial city in western Iran.
Iran agreed to shut down the reactor under the 2015 deal. Iran was allowed to produce a limited amount of heavy water and Tehran has been working on redesigning the reactor.
France, Germany and Britain also criticized the decision in a joint statement.
"We deeply regret the US decision to end the three waivers covering key JCPOA nuclear projects in Iran," read a joint statement from the three European powers.
"These projects, endorsed by UN Security Council Resolution 2231, serve the nonproliferation interests of all and provide the international community with assurances of the exclusively peaceful and safe nature of Iranian nuclear activities."
US Secretary of State Mike Pompeo announced the decision to end the waivers on Wednesday.
The nuclear deal, known formally as the Joint Comprehensive Plan of Action (JCPOA), was signed by the US, Britain, China, France, Germany, and Russia as well as Iran.
However, the US pulled out in 2018 and the latest decision on waivers, following further sanctions, raises the prospect that the agreement could collapse.
Russia and China also blasted the decision by Pompeo, with Moscow saying US foreign policy was becoming "more dangerous and unpredictable".
Speaking at a regular press conference in Beijing on Friday, Chinese Foreign Ministry spokesman Zhao Lijian said the move would hamper “shared efforts” made by parties to the nuclear deal to maintain the agreement.
“It (US decision) demonstrates its consistent pattern of unilateral and hegemonic practice. China is firmly opposed to that,” Zhao added.
In Tehran, Behrouz Kamalvandi, the spokesman of the Atomic Energy Organization of Iran said Thursday Washington's "desperate" decision was aimed at distracting attention from its "continued defeats at the hands of Iran".
“The ending of waivers for nuclear cooperation under (the nuclear deal) will not in practice have any effect on Iran’s work,” Kamalvandi said. “Of course America wants its actions to have an effect in line with pressure on Iran, but in practice nothing will happen.”
Work on redesigning the Arak reactor is continuing, albeit at a slow pace because of sanctions and problems with carrying out the nuclear deal, Kamalvandi said.
AFP and Reuters contributed to this story.