President Obama, in reaching his decision to ditch a missile defense shield in Eastern Europe, used information from a May 2009 National Intelligence Estimate that said Iran would take three to five years longer than originally anticipated to build a long-range missile system, a senior administration official confirmed Friday.

Unclear, however, is whether that estimate was paired with information contained in a "secret" document leaked from the International Atomic Energy Agency that Iran has the ability to make a nuclear bomb and is developing a missile system to carry it.

"We ordered up a full scrub of the intelligence as part of our zero-based review on missile defense," the administration official told FOX News, declining to "read out" any intelligence from the NIE. 

According to Reuters, the NIE deemed Iran unlikely to have intercontinental missile capability until 2015 to 2020, which is further out than the October 2007 NIE that concluded that Iran could develop that long-range capability by 2015.

On Thursday, Obama cited a change in intelligence as his justification to refocus missile defense toward short- and medium-range rockets and to shift to a ship-based system, rather than the ground-based defense shield that was to be placed in Poland and the Czech Republic

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Gen. James Cartwright, vice chairman of the Joint Chiefs of Staff, confirmed to FOX News Thursday that the intelligence assessment used by the president found that Iran would have to test successfully and stage an intercontinental ballistic missile, and would have to have made headway on re-entry issues in order for a threat to be imminent. Iran has not achieved either yet, he said, adding that it takes about three years of testing once Iran has crossed any of these thresholds.  

Iran successfully launched a satellite in February and failed to launch a two-stage solid fuel rocket in May; both actions demonstrate Tehran's intention to develop a long-range missile. 

While military officials see evidence that Iran wants to make progress on long-range missiles, it has not made "as much progress" as previously thought, Cartwright said.

He said that even if Iran buys an ICBM, from North Korea or elsewhere, it will need to stack and test the missiles, which would be a very visible test in the air and would give the United States time to react.

The IAEA document leaked Thursday reveals that Iran has the capacity to build a nuclear bomb, and is working on a delivery system. The contents included information that appears to have originated from intelligence sources in the United States.

According to former U.S. Ambassador to the U.N. John Bolton, the "secret annex" contains information from an Iranian dissident, known as the "laptop informant," who shared details of Iran's bomb-making efforts with the United States.

Bolton, who called the information a significant leak, said it appears from the report that the IAEA confirmed some of the findings of the "laptop informant" and concluded that Iran has enough information to build a bomb.

A senior U.S. official participating at IAEA meetings in Vienna, Austria, said that the internal working document confirms prior allegations unsubstantiated in previous reports from IAEA chief Mohammad El Baradei 

"It captures the belief of all the chief officials on the safeguards department who are convinced that Iran is pursuing a nuclear weapon, that all of what El Baradei called 'alleged studies' in previous reports on Iran is genuine," the official told FOX News.

The official said the report had been very closely held due to "internal political pressure."

"Hallway conversations at the IAEA meetings are focusing on why this document has been suppressed by certain senior figures in the IAEA, notably El Baradei and some figures in the external relations department," the source said. 

The next report on Iran is due at the IAEA Board of Governors meetings in late November.

The decision to move the missile defense shield out of Poland and the Czech Republic was greeted with skepticism by many in Washington, D.C., including Democratic Sen. Claire McCaskill of Missouri.

In a statement late Thursday, McCaskill said the Senate unanimously adopted an amendment in July that stated the U.S. missile defense system should be capable of protecting the United States and Europe. 

"I urge the administration to explain to the American people and our European allies why this decision is in the best interest of our collective security against the Iranian threat -- right now we have been given too little information to be sure that this is the best path forward," she said.

But Cartwright said the ground-based missile defense shield for Poland has not been scrapped, and the Pentagon plans to continue testing it, as has been demonstrated by fiscal year 2010 funding that would allow that option to be kept open.  

Secretary of State Hillary Clinton said on Friday that the United States was never "shelving" its missile defense plan and would never walk away from its allies. She said the new system advances U.S. cooperation with NATO and puts more resources in more countries.

She added that the United States will continue to cooperate closely with Poland on placing a Patriot missile battery there and with the Czech Republic on missile defense research and development.

"As we explore land-base interceptors going forward, we have made it clear that those countries will be at the top of the list. And let me underscore that we are bound together by our common commitment as NATO allies and also by deep historical, economic and cultural ties that will never be broken," Clinton said.

Cartwright said he suspects by the time defense officials look at placing long-range intercept missiles on the ground in Europe they will have moved to an advanced SM-3 model that will basically be an upgraded version of the ground-based system that was planned for Poland. The SM-3 won't be available until 2015, if the testing goes as planned. 

Cartwright said the administration felt that the U.S. had time to develop this upgraded SM-3 if Iran's long-range program was going slower than expected.

But the politically sensitive announcement on Thursday alarmed U.S. allies, particularly the Eastern Europeans, and that could make it difficult to return to request a base in the future for upgraded missiles. 

FOX News' Jennifer Griffin, Mike Emanuel and Nina Donaghy contributed to this report.