Obama defended his administration's record on Israel before clarifying his government's disagreement with Jerusalem. "It's important to realize the depth of the US-Israeli relationship under my administration: billions of dollars have gone to support Israel, including the Iron Dome. The military and intelligence cooperation is unprecedented, that's not our estimation that's from the Netanyahu government."
But he said there was a "substantial disagreement" between his administration and the Israeli government over how to achieve their shared goal of preventing Iran from acquiring nuclear weapons.
"If, in fact, Iran is willing to agree to double-digit years of keeping their program where it is right now and, in fact, rolling back elements of it that currently exist... if we've got that, and we've got a way of verifying that, there's no other steps we can take that would give us such assurance that they don't have a nuclear weapon," he said.
The US goal is to make sure "there's at least a year between us seeing them try to get a nuclear weapon and them actually being able to obtain one," Obama said.
Israel is concerned that Obama's Iran diplomacy, with an end-of-March deadline for a framework nuclear agreement, will still allow Tehran to develop an atom bomb. Iran denies it is seeking nuclear weapons.
Netanyahu has spoken scathingly about a possible deal, saying negotiators appear to have given up on a pledge to prevent Iran from acquiring nuclear weapons. He says a nuclear-armed Iran would pose an existential threat to the Jewish State.
Obama sought to downplay the long-term damage from the row over Netanyahu's speech to Congress, saying the rift was not personal and that he would meet the Israeli leader again if he wins Israel's March 17 election.
"This is not a personal issue. I think that it is important for every country in its relationship with the United States to recognize that the US has a process of making policy," Obama said.
But Obama said Netanyahu had been wrong before with his opposition to a 2013 interim deal with Iran.
"Netanyahu made all sorts of claims. This was going to be a terrible deal. This was going to result in Iran getting 50 billion dollars worth of relief. Iran would not abide by the agreement. None of that has come true.
"It has turned out that in fact, during this period we've seen Iran not advance its program. In many ways, it's rolled back elements of its program."
The White House last week denied a report that the United States and Iran were exploring a possible 10-year deal that would initially freeze Iran's nuclear program but gradually allow it to increase activities that could enable it to produce nuclear arms in the last years of the agreement.
In a speech on Monday to the American Israel Public Affairs Committee (AIPAC), the largest US pro-Israel lobby, Netanyahu again warned that a nuclear deal could threaten Israel's survival while insisting the US-Israeli relationship was "stronger than ever."
Asked about the prospects for a final deal with Iran, which has a June 30 deadline, Obama said that a key doubt was whether Iran would agree to rigorous inspection demands and the low levels of uranium enrichment capability they would have to maintain.
"But if they do agree to it, it would be far more effective in controlling their nuclear program than any military action we could take, any military action Israel could take and far more effective than sanctions will be," Obama said.
A comprehensive nuclear deal is seen as crucial to reducing the risk of a wider Middle East war, at a time when Iran is deeply involved in conflicts in Syria and Iraq.