Newspaper editorials decried the visit as American "meddling" and said it was ill-timed. Protesters in at least three cities burned U.S. flags and waved banners demanding the envoys go home.
Meanwhile, an American newspaper reported that a recent increase in U.S. air strikes in Pakistan's tribal areas was a result of U.S. worries that the new government would scale back military operations in the area.
Such strikes have killed at least 25 people this month, sparking anger over civilian casualties in the region, where Osama bin Laden and other al Qaeda operatives could be hiding.
Washington has been scrambling to build bridges with Pakistan's new leaders, who routed Musharraf's loyalists in parliamentary elections last month partly because of popular anger over the president's alliance with the U.S. in its war on terror.
The new government has pledged to slash Musharraf's powers and review his American-backed counterterrorism policies. Already, partners in the new government have said they would negotiate with some militant groups - an approach that has drawn criticism from Washington, which has provided about US$10 billion in aid to Pakistan since 2001.
The U.S. envoys, Deputy Secretary of State John Negroponte and Assistant Secretary of State Richard Boucher, began meetings in Islamabad just as newly elected Prime Minister Yousaf Raza Gilani was taking his oath of office Tuesday.
Thursday's English-language newspaper Dawn said the envoys came to Pakistan "in indecent haste." The visit was "not in keeping with diplomatic propriety," it said in an editorial.
The newspaper News urged U.S. officials to "restrain themselves in further meddling in Pakistan's affairs."
Negroponte countered that there was "no hidden agenda" in his visit and that he had "no desire to interfere or intervene in any way in political arrangements which are developing" in Pakistan.
American military actions inside Pakistan have also drawn anger and charges of interference. A Thursday report in The Washington Post cited unidentified U.S. officials as saying that the uptick in U.S. air strikes was aimed at inflicting maximum damage on militant networks in the tribal regions before Musharraf's powers are diminished under the new government.
Negroponte and Boucher traveled Wednesday to the lawless northwest border region where the air strikes have hit, visiting U.S.-funded border guards and as well as a mountaintop paramilitary base at the Khyber Pass, the U.S. Embassy said.
On Thursday, they traveled to the southern city of Karachi to meet with provincial officials and the American business community there, the embassy said.
Meanwhile, a U.S. congressional delegation met Thursday with Musharraf, but made no public comments. Six lawmakers were in Pakistan after a two-day visit in neighboring Afghanistan.
Local TV channels said Negroponte and Boucher met Wednesday with commanders of the Frontier Corps, the paramilitary force that Washington plans to train and equip to fight militants, and also with tribal leaders.
"We have to fight terrorism," Gilani later told the American diplomats at his home in Islamabad. "We will confront it with complete determination."
But "the world community has to do more in order to develop a collective approach" to the problem, Gilani said, stressing the need for economic development to help tackle extremism. He repeatedly addressed Negroponte as "your excellency."
Rasul Bakhsh Rais, who teaches political science at the University of Management Sciences in Lahore, said Negroponte and Boucher's visit was "not at the appropriate time." The new Cabinet lineup is not expected to be announced before this weekend.
"The locus of authority has changed in Pakistan and they (the Americans) have to look toward new political forces," Rais said.