Earlier, diplomats had confirmed that Negroponte would appeal to Musharraf to call off the emergency with immediate effect, to quit the army, hold elections on time, lift media restrictions and release political prisoners.
Swat valley clashes
Musharraf has said that the emergency order was imposed to combat armed groups in Pakistan linked to al-Qaeda and the Taliban.
He is under pressure due to the Pakistani army's losses in recent fighting with pro-Taliban fighters in the Swat valley region.
Bays said that the US is concerned about the gains the pro-Taliban fighters have made particularly in the Swat Valley.
The Pakistan army said on Saturday that it had killed up to 40 fighters in the area but forces loyal to Maalana Fazlullah, a Muslim religious leader, have captured several villages, police stations and government buildings.
Washington has granted $10bn in aid to Pakistan since 2001, when Musharraf pledged support to the US-led "war on terror".
Musharraf has told BBC that Pakistan's nuclear weapons will not be allowed to fall into the wrong hands while the military is in control of them.
In an interview, aired on Saturday, he said said that if elections were held in a "disturbed environment", it could bring in dangerous elements who might endanger Pakistan's "strategic assets".
Musharraf said: "They [the nuclear weapons] cannot fall into the wrong hands, if we manage ourselves politically. The military is there - as long as the military is there, nothing happens to the strategic assets, we are in charge and nobody does anything with them."
Shortly after he arrived on Friday evening, Negroponte spoke to Benazir Bhutto, leader of the opposition Pakistan People's Party (PPP), by telephone.
She had been freed from house arrest in Lahore hours earlier, before Musharraf swore in an interim prime minister and cabinet.
|Bhutto says she will not work under Musharraf's|
rule, whether he quits the army or not [AFP]
Musharraf has pledged to hold elections by January 9 but has indicated that electioneering will be held under emergency rule.
The decision to maintain emergency and suspend the constitution has angered opposition leaders who say their campaigns cannot be run effectively under the restrictions.
Bhutto has rejected the interim government and is in talks with other opposition leaders in an effort to form a united front to force Musharraf from office.
Washington had supported a mooted power-sharing deal between Bhutto and Musharraf but the PPP leader put an end to talks this week, saying she would never ally herself to the president.
In another development on Saturday, media authorities in Dubai said they were considering whether to allow Geo and ARY One World, two leading private Pakistani news channels, to resume broadcasting after shutting them down the day before.
Both channels went off air at 1am local time (0800 GMT) on Saturday.
"We are in contact with them ... to see if there is a possibility to (allow them to) resume" broadcasting, Amina Rustamani, head of Dubai's media watchdog, told AFP.
The channels, ordered off air during emergency rule, said they had been forced to close down altogether after being ordered to halt transmissions via the UAE, a federation of seven emirates including Dubai.
Geo and ARY One World both have offices and studios in Dubai Media City, from where they broadcast news.