The NATO chief's comments were in response to a BBC interview with Karzai in which the Afghan leader argued the country was worse off, politically and security-wise, since U.S. and allied troops invaded Afghanistan in 2001.
"What we wanted was absolute security and a clear-cut war against terrorism," Karzai said at the time.
What Afghanistan got was continued violence and civilian deaths due to combat operations by American and NATO forces, he added.
But Rasmussen said Karzai's take on the war was not one shared by Afghans across the country.
"We have sacrificed much in blood and treasure to assist the Afghan people, and ... whenever I meet Afghans, they express appreciation for that,” according to Rasmussen.
The increasingly heated rhetoric between Washington, Brussels and Kabul come as U.S. and allied leaders remain at a stalemate over a postwar deal with the Karzai government.
The agreement will lay the groundwork for a postwar American force and grant legal immunity for U.S. troops in that force.
Lack of immunity for U.S. troops was a crucial factor in the failed attempt to set up a postwar security deal in Iraq, and it set the stage for the recent wave of sectarian violence against Iraqi forces and civilians in the country.
There are roughly 55,000 U.S. troops in Afghanistan, but most are expected to go back to the United States over the coming months.
The final American units will return stateside after the April 2014 presidential election, marking the end of the American war in Afghanistan.
U.S-Afghanistan negotiations for a postwar American presence after the White House-mandated withdrawal in 2014 have been fraught with disagreements and frayed relations between the two countries since they began in 2011.
Most recently, Washington's plan to have U.S. special operations forces and American intelligence operatives conduct missions against the Taliban and al Qaeda elements inside Afghanistan after the White House's 2014 withdrawal deadline is "a deal breaker," according to Aimal Faizi, spokesman for Karzai.
But a former top Afghan government official warned that if Kabul and Washington cannot agree on the rest of the postwar security deal, known inside the Pentagon as a bilateral security agreement, the country will fall apart.
"All that has been invested in blood and treasure will go with the wind, and the destiny of this country will go back to square one," Afghanistan's former defense minister Gen. Abdul Rahim Wardak told The Associated Press on Thursday.