"We are committed to that special bond, and we are going to do what's required to back that up, not just with words, but with actions.''
Netanyahu said reports of the demise of the US-Israeli relationship were "flat wrong".
Tuesday's meeting, which included a lengthy working lunch, was considerably warmer than the last time the two men met.
"We are committed to that special bond, and we are going to do what's required to back that up, not just with words, but with actions'
Netanyahu was reportedly denied the privileges normally given visiting foreign dignitaries when he visited the White House in March, including the ritual hand-shake in front of photographers.
That visit was soured by Israel's announcement of plans for 1,600 new settlement homes in occupied East Jerusalem during a visit by Joe Biden, the US vice-president, a move Washington called "insulting" and led to the tone between the long-standing allies growing increasingly frosty.
Israel also came under heavy international pressure, including from Obama and other senior US officials, to loosen its three-year-old blockade of the Palestinian territory of Gaza after its deadly military raid on a flotilla trying to break the embargo on May 31.
Obama had called the Gaza situation "unsustainable" and Israel on Tuesday confirmed that it was easing its blockade on Gaza, allowing the import of consumer goods.
But it maintained restrictions on "weapons, war material and dual-use items", including construction materials needed for rebuilding after Israel pounded Gaza in a 22-day war early last year.
Al Jazeera's Rosalind Jordan, reporting from Washington DC, said the Obama administration considered Tuesday's meeting extremely important.
"There is universal belief here in Washington that this is a chance to reset the relationship between the Obama administration and the Netanyahu administration," our correspondent said.
Looming US elections
Observers believe that with November's US congressional elections just around the corner, Obama is unlikely to risk more public disagreements with Netanyahu, given that many US politicians, including from his Democratic party, draw significant support from pro-Israeli groups.
Binyamin Netanyahu, Israeli prime minister, on reports of the demise of US-Israeli ties
But Fawaz Gerges, a professor at London School of Economics told Al Jazeera that "many voices in America now are saying Israel represents a strategic liability rather than a security asset for the United States".
"What the Americans now are saying is - and this is a very important point - is that what happens in the Israeli-Palestinian theatre affects the national security of United States," he said.
Obama publicly assured Netanyahu of his commitment to Israel's "unique security requirements" on Tuesday and said he would never ask it to take steps that would jeopardise its safety.
The US administration sparked Israeli concerns in May by acceding to demands at a UN meeting on the Nuclear Non-proliferation Treaty that the final document urge Israel to sign the pact.
Israel is believed to have the Middle East's only nuclear arsenal but will not confirm or deny it.
The White House said on Tuesday that Obama would oppose efforts to single out Israel at a conference of the International Atomic Energy Agency in September.
Underlying the friendly tone between the two men on Tuesday, Netanyahu invited Obama to make his first presidential visit to Israel.
"I'm ready, anytime," Obama responded, but neither leader set a date.