An Israeli official told Reuters on condition of anonymity that Netanyahu's aides had asked for a meeting when he visits the United Nations this month and "the White House has got back to us and said it appears a meeting is not possible. It said that the president's schedule will not permit that."
Netanyahu has met Obama on all but one of his U.S trips since 2009. The president was on a foreign visit when the prime minister came to the United States in November 2010.
He argues that setting a clear boundary for Iran's uranium enrichment activities and imposing stronger economic sanctions could deter Tehran from developing nuclear weapons and mitigate the need for military action.
In comments that appeared to bring the possibility of an Israeli attack on Iran closer, Netanyahu had earlier taken Washington to task for rebuffing his call to set a "red line" for Iran's nuclear programme, which has already prompted four rounds of U.N. sanctions.
"The world tells Israel 'wait, there's still time'. And I say, 'Wait for what? Wait until when?'" said Netanyahu, speaking in English.
"Those in the international community who refuse to put red lines before Iran don't have a moral right to place a red light before Israel," he added, addressing a news conference with Bulgaria's prime minister.
The website of Israel's daily newspaper Haaretz called his words "an unprecedented verbal attack on the US government".
Iran makes no secret of its hostility to Israel, widely assumed to be the region's only nuclear-armed power, but says its nuclear programme is purely peaceful.
Netanyahu's relations with Obama have been strained over Iran and other issues, such as Jewish settlement building in the occupied West Bank.
But he has never framed his differences with Obama - who has pledged he will "always have Israel's back" and is deep in a re-election campaign - in moral terms.
Republican challenger Mitt Romney has accused Obama of throwing Israel "under the bus".
Netanyahu's comments followed US Secretary of State Hillary Clinton's remarks on Monday that the United States would not set a deadline in further talks with Iran, and that there was still time for diplomacy to work.
Diplomats have also said six world powers - including the United States - are poised to voice "serious concern" about Iran's uranium enrichment programme and to urge it to open up access to nuclear sites.
U.S. Defense Secretary Leon Panetta said on Tuesday that Washington would have little more than a year to act to stop Iran if it decided to produce a nuclear weapon.
Iran has threatened to retaliate against Israel and US interests in the Gulf if it is attacked, and any such conflict could throw Obama's re-election bid off course.
Netanyahu did not mention Clinton by name but pointedly parroted her use of the word "deadline", saying:
"If Iran knows that there is no 'deadline', what will it do? Exactly what it's doing. It's continuing, without any interference, towards obtaining a nuclear weapons capability and from there, nuclear bombs ...
"So far we can say with certainty that diplomacy and sanctions haven't worked. The sanctions have hurt the Iranian economy but they haven't stopped the Iranian nuclear programme. That's a fact. And the fact is that every day that passes, Iran gets closer and closer to nuclear bombs."
Recent tougher Israeli rhetoric has stoked speculation that Israel might attack Iran before the U.S. election in November, believing that Obama would be forced to give it military help to avoid alienating pro-Israeli voters.
But over the past week, Netanyahu, in calling for a "red line", had appeared to be backing away from military action and preparing the ground for a possible meeting with Obama.
Opinion polls suggest that a majority of Israelis do not want their military to strike Iran without U.S. support.
Defence Minister Ehud Barak seemed to criticise Netanyahu's assault on the Jewish state's biggest ally.
"Despite the differences and importance of maintaining Israel's independence of action, we must remember the importance of partnership with the United States and try as much as possible not to hurt that," a statement from his office said.
