WASHINGTON — Deputy Secretary of State John Negroponte told Congress today that President Musharraf of Pakistan is an “indispensable” ally in the American-led war on terrorism and that “partnership with Pakistan and its people is the only option.”

In prepared testimony, Mr. Negroponte also told the House Foreign Affairs Committee that administration officials “strongly disagree” with General Musharraf’s crackdown on his political opponents.

“We strongly counseled against emergency rule, but Pakistan’s leadership did not follow our advice,” Mr. Negroponte said.

His remarks echoed the Bush administration’s position in the days since General Musharraf declared emergency rule.

The administration’s public response to the crisis in Pakistan has been mild and measured, out of concern of going too far in rebuking a close anti-terrorism ally. It stands in sharp contrast to how the administration responded when Burma’s military regime cracked down on pro-democracy protesters in September, for instance.

While he acknowledged an ongoing review of American aid to Pakistan in light of the crisis, Mr. Negroponte did not announce any changes to American policy.

“Pakistan has undoubtedly made progress toward becoming a more moderate, stable, and prosperous country since President Musharraf came to power, and that is why we are so concerned that the backsliding inherent in the state of emergency be reversed before it damages these positive trends,” Mr. Negroponte said.

Mr. Negroponte faces a skeptical Democratic-led Congress. Many lawmakers say America should consider cutting off foreign aid to Pakistan and that General Musharraf shouldn’t be so readily praised.

Senator Kerry, Democrat of Massachusetts, a member of the Foreign Relations Committee, planned to offer a resolution condemning General Musharraf’s actions, while others said military aid should be withheld.

“We have the worst of all possible worlds,” Rep. Gary Ackerman, Democrat of New York, who chairs the panel’s subcommittee on Middle East and South Asia, said. “Our ally is an isolated and deeply resented leader who is less popular with his own people than Osama bin Laden.”