Pakistani television station Geo at the weekend, were "misinterpreted".
Karzai has said that his country would support Pakistan if it was attacked by either the United States or India.
"God forbid, If any time war erupts between Pakistan and America, Afghanistan will side with Pakistan," Karzai said in an interview aired late Saturday.
The prospect of all-out conflict between the US and Pakistan remains remote, despite strained relations in recent months, following the killing of Osama bin Laden by US commandos in a secret raid in a Pakistani garrison town.
Nevertheless the comments raised eyebrows among Western officials in Kabul allied to the 10-year campaign to keep the Taliban from returning to power.
Christopher Chambers, a NATO spokesman, told reporters in Kabul that "we all need to focus on much wider dialogue that's required for peace... and which the people of both countries mostly certainly want and certainly deserve."
The palace insisted the remarks were broadcast out of context.
"Pakistani media has misinterpreted it," said the president's deputy spokesman Seyamak Herawi.
"They only showed the first part when the president says Afghanistan will back Pakistan if there is a war."
Instead, the reference was to Afghanistan's willingness to house refugees from Pakistan in case of any conflict, in the way that millions of Afghans are given refuge across the border in Pakistan's northwestern frontier region.
"But in connection with the war on terrorism if there is a war on Pakistan, Afghanistan will not support that," he further stated.
Relations between Pakistan and Afghanistan have been long-tested, with Karzai recently accusing his neighbour of playing a "double-game" with Afghan insurgents fighting the US-led war effort who hold bases across the border.
In the Geo interview, Karzai also sought to assuage Pakistani fears over US influence in the region following the drawdown of Western combat forces by the end of 2014 and restated his conditions for a long term US partnership.
Afghanistan's conditions for a US deal include that American troops must not enter Afghan homes, implying that they should end controversial night raids in pursuit of Taliban targets that have caused many civilian casualties.