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.
BBC NEWS | South Asia | Al-Qaeda 'rebuilding' in Pakistan
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.
