In a news conference before departing Pakistan, Negroponte said he hoped that Musharraf would listen to his appeal to end a crackdown on opponents before legislative elections scheduled for January.
"I urged the government to stop such actions, lift the state of emergency and release all political detainees," Negroponte told reporters at the US embassy.
"Emergency rule is not compatible with free, fair and credible elections."
But Musharraf has appeared intent on setting his own pace despite warnings from Washington, which has been hesitant to match criticism with actions such as cutting military aid.
Gains by fighters have raised US concerns about Pakistan's ability to combat militancy and flush out remnants of al-Qaeda and the Taliban believed to be sheltering in the country's rugged northwestern tribal areas.
Pakistani army helicopters strafed positions in the northwest on Sunday, hitting a valley where fighters loyal to a pro-Taliban cleric have been battling security forces for months, the army said.
|Gains by fighters have raised US concerns |
about Pakistan's ability to combat militancy
Soldiers also fired artillery and mortar shells at fighters in Swat, inflicting "many casualties", the army said.
Fighters loyal to Maulana Fazlullah, a rebel cleric who wants to impose Islamic rule, have steadily advanced down the Swat valley since July, taking over towns and driving back government forces.
Musharraf has insisted he will only lift the emergency if the national security situation improves, and strongly hinted that such a move was unlikely before parliamentary elections scheduled to be held by January 9.
US nuclear security
His government's response to Negroponte's remarks came on the same day that a US newspaper reported that the US was helping Pakistan keep its nuclear weapons secure in a top-secret programme that has cost Washington almost $100m.
The US programme was reportedly created after the attacks of September 11, 2001 when the US Musharraf as a key ally in its "war on terror".
The New York Times, citing unidentified current and former senior officials, said that for six years, the US has provided equipment and training to ensure that security remains tight for Pakistan's nuclear arms.
It said it had know about the programme - buried in secret portions of the federal budget - for more than three years but had held off publication on a request from the Bush administration, which feared repercussions for national security.
But Pakistani media reports have shed light on the programme and the White House withdrew its demand against publication last week, while remaining unwilling to discuss details of it, the paper said.