The incident has thrown the already fragile US-Pakistan ties into a tizzy, with Pakistan boycotting the Bonn conference to discuss the future of Afghanistan.
"Earlier today the President placed a phone call to Pakistani President Asif Ali Zardari to personally express his condolences on the tragic loss of twenty-four Pakistani soldiers this past week along the border of Afghanistan and Pakistan," the White House said in a statement.
"The President made clear that this regrettable incident was not a deliberate attack on Pakistan and reiterated the United States' strong commitment to a full investigation," the White House said.
During the roughly 30-minute call, the two presidents reaffirmed their commitment to the US-Pakistan bilateral relationship, which is critical to the security of both nations, and they agreed to stay in close touch, said the statement.
The cross border attack, that the US has described as 'unintended', led Pakistan to close the NATO supply routes through its territory in protest. Following the attack Pakistan Army chief Ashfaq Pervez Kayani also gave the army full liberty to retaliate in similar cases in the future.
Top Pakistani officials have said that Islamabad needs to review its relations in the wake of the incident described by the army as "a blatant act of aggression".
"We'll let Zardari's office tell you what he said," a senior administration official said when asked what the response from the Pakistani president was.
"The presidents discussed the decisions Pakistan recently announced with regards to reviewing our security relationship and President Obama expressed our commitment to working through these issues in a manner that is most beneficial to both countries," the official told PTI on condition of anonymity.
Following the incident, Pakistan also ordered the US to vacate the Shamsi airbase, that was reportedly being used by CIA-operated drones. The US today started pulling out its nationals from the airbase amidst strict security.