By Jonathan Landay

WASHINGTON (Reuters) - The United States and its negotiating partners agreed "in secret" to allow Iran to evade some restrictions in last year's landmark nuclear agreement in order to meet the deadline for it to start getting relief from economic sanctions, according to a think tank report published on Thursday.

The report, which was released by the Washington-based Institute for Science and International Security, is based on information provided by several officials of governments involved in the negotiations. The group's president David Albright, a former U.N. weapons inspector and co-author of the report, declined to identify the officials, and Reuters could not independently verify the report's assertions.

"The exemptions or loopholes are happening in secret, and it appears that they favor Iran," Albright said.

(Link to the report: http://isis-online.org/isis-reports/detail/jcpoa-exemptions-revealed)

The report ignited a chorus of Republican criticism, including from the campaign of presidential nominee Donald Trump. His campaign sought to link the findings to Trump's Democratic opponent, Hillary Clinton, who was secretary of state when secret talks were held with Iran but had left office before formal negotiations began.

"The deeply flawed nuclear deal Hillary Clinton secretly spearheaded with Iran looks worse and worse by the day," said a statement issued by retired Army General Michael Flynn, a top Trump adviser. "It’s now clear President Obama gave away the store to secure a weak agreement that is full of loopholes."

The Clinton campaign did not immediately comment on the report.

The White House said it took "significant exception" to some of the report's findings, saying that the easing of sanctions was always dependent upon Iran's adherence to the agreement.

"The implementation date was driven by the ability of the (International Atomic Energy Agency) to verify that Iran had completed the steps that they promised to take," White House spokesman Josh Earnest told reporters at a briefing on Thursday.

"That is what precipitated implementation day. Since then Iran has been in compliance with the agreement," Earnest said.

Among the exemptions outlined in the think tank's report were two that allowed Iran to exceed the deal's limits on how much low-enriched uranium (LEU) it can keep in its nuclear facilities, the report said. LEU can be purified into highly enriched, weapons-grade uranium.

The exemptions, the report said, were approved by the joint commission the deal created to oversee implementation of the accord. The commission is comprised of the United States and its negotiating partners -- called the P5+1 -- and Iran.

One senior "knowledgeable" official was cited by the report as saying that if the joint commission had not acted to create these exemptions, some of Iran’s nuclear facilities would not have been in compliance with the deal by Jan. 16, the deadline for the beginning of the lifting of sanctions.

The U.S. administration has said that the world powers that negotiated the accord -- the United States, Russia, China, Britain, France and Germany -- made no secret arrangements.

A White House official, speaking on condition of anonymity, said the joint commission and its role were "not secret." The official did not address the report's assertions of exemptions.

State Department spokesman John Kirby said that Iran was not granted "exceptions" to limits on low-enriched uranium or heavy water "that would allow them to have a usable amount of material in excess of what they're supposed to have towards the production of fissile material."

He repeatedly declined to directly address the report's findings on the exemptions, saying the joint commission's work is "confidential."

Diplomats at the United Nations for the other P5+1 countries did not respond to Reuters' requests for comment on the report. Iranian officials were not immediately available for comment.

Albright said the exceptions risked setting precedents that Iran could use to seek additional waivers.

Albright served as an inspector with the U.N. International Atomic Energy Agency (IAEA) team that investigated former Iraqi President Saddam Hussein's nuclear weapons program.

While Albright has neither endorsed nor denounced the overall agreement, he has expressed concern over what he considers potential flaws in the nuclear deal, including the expiration of key limitations on Iran's nuclear work in 10-15 years.

EXEMPTIONS ON URANIUM, "HOT CELLS"

The administration of President Barack Obama informed Congress of the exemptions on Jan. 16, said the report. Albright said the exemptions, which have not been made public, were detailed in confidential documents sent to Capitol Hill that day -- after the exemptions had already been granted.

The White House official said the administration had briefed Congress "frequently and comprehensively" on the joint commission's work.

Democratic Senator Robert Menendez, a leading critic of the Iran deal and a senior member of the Senate Foreign Relations Committee, told Reuters in an email: "I was not aware nor did I receive any briefing (on the exemptions).”

As part of the concessions that allowed Iran to exceed uranium limits, the joint commission agreed to exempt unknown quantities of 3.5 percent LEU contained in liquid, solid and sludge wastes stored at Iranian nuclear facilities, according to the report. The agreement restricts Iran to stockpiling only 300 kg of 3.5 percent LEU.

    The commission approved a second exemption for an unknown quantity of near 20 percent LEU in "lab contaminant" that was determined to be unrecoverable, the report said. The nuclear agreement requires Iran to fabricate all such LEU into research reactor fuel.

If the total amount of excess LEU Iran possesses is unknown, it is impossible to know how much weapons-grade uranium it could yield, experts said.

The draft report said the joint commission also agreed to allow Iran to keep operating 19 radiation containment chambers larger than the accord set. These so-called "hot cells" are used for handling radioactive material but can be "misused for secret, mostly small-scale plutonium separation efforts," said the report. Plutonium is another nuclear weapons fuel.

The deal allowed Iran to meet a 130-tonne limit on heavy water produced at its Arak facility by selling its excess stock on the open market. But with no buyer available, the joint commission helped Tehran meet the sanctions relief deadline by allowing it to send 50 tonnes of the material -- which can be used in nuclear weapons production -- to Oman, where it was stored under Iranian control, the report said.

The shipment to Oman of the heavy water that can be used in nuclear weapons production has already been reported. Albright's report made the new assertion that the joint committee had approved this concession.

(Additional reporting by Patricia Zengerle, Arshad Mohammed, Roberta Rampton and Amanda Becker; editing by Stuart Grudgings)