Discontent in Washington
Read between the lines here. It is not altogether becoming of a departing intelligence chief to launch a political storm, but the signs are that the US is growing increasingly discontent with the Musharraf regime. Yes, it wants a scapegoat, but the signs are that it is deliberately drawing back from the Pakistan regime with it was once so close.
The BBC's James Westhead in Washington says that until now the US has not been so specific about where it believes al-Qaeda's leaders are hiding.
Such a claim will be embarrassing for Pakistani President Pervez Musharraf, who Mr Negroponte described as a key partner in America's war on terror, our correspondent says.
Afghanistan has welcomed the comments. President Hamid Karzai's chief-of-staff, Jawed Ludin, told the BBC that Afghanistan had long maintained that the Islamic militants operated from within Pakistan, and that Mr Negroponte's statement was refreshing in its honesty.