ISLAMABAD — The resignation of Pervez Musharraf as president of Pakistan has left a void in American-Pakistani relations at a critical time when Western security officials claim that Al Qaeda has rebuilt its sanctuary on the country’s border with Afghanistan.

A suicide bomber blew himself up yesterday at a hospital in a northwestern Pakistani town killing at least 23 people. Five soldiers and 13 Taliban militants were killed in the Bajaur tribal region bordering Afghanistan.

Relations with Pakistan and America got off to a rocky start after the September 11, 2001, attacks. The American deputy secretary of State at the time, Richard Armitage, forced Mr. Musharraf to reverse his country’s pro-Taliban policy.

The relationship between the two allies was characterized by frustration, resentment, and distrust. But the partnership, however flawed, delivered to America limited access to Pakistan’s nuclear program and the arrest of some leading Al Qaeda members.

A senior Western military official based in Islamabad, the capital, said the alliance had also helped to foster deeper links with the Pakistan’s senior military command, in particular, the army chief, General Ashfaq Kiyani.

But Mr. Musharraf failed to galvanize popular support for the “war on terror” and is suspected of allowing military intelligence to play a double game by maintaining covert support for jihadis and the Taliban.

If true, it has been a ruthlessly cynical policy as Pakistan has sacrificed nearly 2,000 soldiers and paramilitaries fighting in its tribal areas.

The former president most probably harbored a belief commonly held among Pakistan’s top brass: that America’s anti-terror policy is insincere and is mainly a mask for its strategic regional designs.

The New York Times quoted a senior White House official in a report yesterday who regretted that America had “stuck with Mr. Musharraf for too long and developed few other relationships in Pakistan.”

Washington will continue its fraught relationship with Pakistan’s military but it will have to forge a new one with its civilian coalition government.

Pakistan’s ambassador to Washington, Hussain Haqqani, was one of the lobbyists who attempted to sell America the idea of “democracy as counter-insurgency.”

His argument was that a popularly elected government would be able to win support for counter-terrorism operations more effectively.

However, the coalition government has so far proven itself incapable of governing as its two main partners been engrossed in horse-trading and bickering.

After taking power in March, the government tried to use negotiations instead of force to end violence across the country. The negotiations brought a lull in violence but also raised concern among allies and in Afghanistan that the talks would only give militants breathing space to regroup and organize cross-border attacks on Western forces in Afghanistan.

A political analyst and newspaper editor, Najam Sethi, said, “This is an unpopular war. That is why the army and Mr. Musharraf quickly handed over its ‘ownership’ to the civilians shortly after the government was formed. I don’t think Asif Ali Zardari [leader of the dominant Pakistan Peoples Party] will have the time or the inclination to articulate an anti-terror policy that satisfies America.”