But the Israeli leader arrived and left without making the customary public appearance with the US president, and with no press conference.
"The president reaffirmed our strong commitment to Israel's security, and discussed security cooperation on a range of issues," the White House said in a brief statement afterwards.
"The president and prime minister also discussed Iran and how to move forward on Middle East peace."
Netanyahu dismissed reports of tension between him and Obama, twice calling the meeting "positive".
The meeting was "very positive and focused. It dealt with an array of important issues including the joint effort to advance the peace process," he told reporters, stressing: "I think the visit will prove to be very important."
Ahead of the meeting, Netanyahu said he was ready to immediately start peace negotiations with the Palestinians, but prospects appear dim.
Piling the pressure on the US administration, senior aides to Palestinian president Mahmud Abbas said Tuesday he could quit if US efforts to relaunch Middle East peace talks stay deadlocked.
Such a move could lead to a collapse of the Palestinian Authority,
"If president Abbas feels that his project of establishing a Palestinian state is in danger and that Israel wants to destroy the idea of a Palestinian state, then I think he will not remain in the position of the presidency," Palestinian chief negotiator Saeb Erakat told AFP.
Abbas already announced last week he would not stand for re-election in January with aides putting it down to his frustration with the US stance on settlements.
It followed US Secretary of State Hillary Clinton praise for Netanyahu's offer of a limited easing of settlement construction as "unprecedented," triggering Arab fury.
Clinton later backtracked, but her statements were widely interpreted as a U-turn by Washington.
A senior State Department official William Burns reiterated Tuesday that a freeze on settlements remained the US position.
"We do not accept the legitimacy of continued Israeli settlements," Burns told a Middle East Institute conference here, saying, "it obviously falls short of... a full settlement freeze."
He stressed the US "goal is clear, two states living side by side in peace in security."
The number of Jewish settlers living in the occupied West Bank including east Jerusalem has doubled since the Oslo peace process began, and the Palestinians fear further growth could make it impossible to establish a viable state.
A senior Fatah official told AFP Tuesday that establishing the borders of a Palestinian state would be one way to resolve the dispute over settlements.
Mohammed Dahlan, a leading member of Palestinian president Abbas's secular movement, told AFP: "We want to carry out serious negotiations for a two-state solution with a clear timetable not exceeding two years.
"But before that we need the international community to announce an agreement on the borders of the two states.... That would solve the problem of settlements and the problem of Jerusalem."
Netanyahu on Monday urged Abbas to start immediate negotiations.
"I say today to Mahmud Abbas, the leader of the Palestinian Authority, 'let us seize the moment to reach an historic agreement. Let us begin talks immediately,'" he told a conference of North American Jewish leaders.
Israeli Defense Minister Ehud Barak was also in Washington for talks with his US counterpart Robert Gates and US special envoy to the Middle East George Mitchell.
The State Department said the meeting between Barak and Mitchell was part of the "same phase" as Clinton's talks in the region last week.
"We continue to encourage the parties to get into negotiations as soon as possible, but we recognize that there are gaps that still exist and we continue to work to clarify and close those gaps," said State Department spokesman Phillip Crowley.
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Image: AFP: Chip Somodevilla.