The conversation followed the Israeli leader's harsh criticism of the Obama administration's refusal to set deadlines for Tehran.
The White House readout from the hourlong conversation between the two leaders made no mention of Netanyahu's sharp comments.
"The two leaders discussed the threat posed by Iran's nuclear program, and our close cooperation on Iran and other security issues," the statement said. "President Obama and Prime Minister Netanyahu reaffirmed that they are united in their determination to prevent Iran from obtaining a nuclear weapon, and agreed to continue their close consultations going forward.
"Contrary to reports in the press, there was never a request for Prime Minister Netanyahu to meet with President Obama in Washington, nor was a request for a meeting ever denied."
Speaking to reporters early Tuesday, Netanyahu condemned U.S. Secretary of State Hillary Clinton's weekend comment on Bloomberg Radio that, "We're not setting deadlines," when asked if the administration could outline consequences should Iran refuse to comply with the U.N. Security Council's repeated requests to halt its uranium enrichment program.
U.S. State Department spokeswoman Victoria Nuland restated Obama's commitment to keep Iran from building nuclear weapons Monday, saying, "It is not useful to be parsing it, to be setting deadlines one way or another, red lines."
Netanyahu bristled at the U.S. resistance to issuing a deadline.
"The world tells Israel, 'Wait, there's still time.' And I say, wait for what? Wait until when?" he said. "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."
His remarks threatened to elevate Iran's nuclear program as a U.S. presidential campaign issue and laid bare a thinly disguised conflict between Israel and the United States over how to deal with Iran, The New York Times said Tuesday, adding Netanyahu's government has threatened to bomb suspected Iranian enrichment sites.