Negroponte's visit to Pakistan, his second in three months, is officially part of a U.S.-Pakistan strategic dialogue focusing on various fields, including counterterrorism.
Washington has recently stepped up pressure on Musharraf to tackle Al-Qaeda and Taliban militants on Pakistani soil, threatening to launch unilateral strikes.
The visit also comes amid political turmoil following the expulsion of former Prime Minister Nawaz Sharif hours after he arrived in Pakistan on September 10 after seven years in exile.
RFE/RL's Radio Free Afghanistan reports that Negroponte met with Afghan President Hamid Karzai on September 11 during a visit to Afghanistan.
After the talks, Negroponte said the United States is keeping an eye on the reported presence of Iranian weapons in Afghanistan.
"We are concerned by reports, which we consider to be reliable, of explosively formed projectiles and other kinds of military equipment coming from Iran across the border and coming into the hands of the Taliban," Negroponte said.
Negroponte also said he thinks Al-Qaeda leader Osama bin Laden is still alive and is hiding in the Pakistan-Afghanistan border area.
(with agency reports)