Speaking to reporters in Islamabad, Ryan Crocker contradicted comments in a video interview posted on a website last week in which al-Qaida's deputy leader, Ayman al-Zawahiri, said Bin Ladin was still leading the group's war on the West.
"I think that Osama bin Ladin is no longer the operational head of al-Qaida, because he is hiding deep inside the mountains and he doesn't have contact with the al-Qaida people," Crocker said.
Referring to al-Zawahiri, he added: "I don't know if al-Zawahiri is heading al-Qaida or not; what I do know is that al-Qaida is in serious trouble these days."
US officials have long said they believe Bin Ladin masterminded the September 11 attacks and has been hiding along the rugged Pakistan-Afghanistan border since US forces failed to capture him after invading Afghanistan in late 2001.
Asked about Pakistani President Pervez Musharraf's announcement that a senior al-Qaida figure, Abu Hamza Rabia, was killed in a tribal region bordering Afghanistan this month, Crocker echoed comments by other US officials.
"I don't know what happened, but if President Musharraf is saying he is dead, we must trust what President Musharraf is saying," he said.
President Musharraf is an ally
of the US in its war on terror
The Pakistani authorities say Rabia was killed when bomb-making material stored at his hideout was detonated accidentally and comrades took away his body.
Villagers in the area said the blast was caused by a missile fired from an unidentified aircraft, possibly a US drone, and that two children died in the blast.
Last week unidentified armed men siezed a journalist who had reported that Rabia was killed by a US missile and who took photographs of what villagers said were fragments of the weapon.
Crocker also said the US expressed concern that Pakistan had allowed a prominent anti-American group to take a role in providing relief to survivors of the catastrophic earthquake that hit northern Pakistan on 8 October.
"This is not good. Jamat-ud-Daawa is the new name of Lashkar-e-Taiba. I think that these groups should not be allowed to join the relief operations. The government of Pakistan should make use of other NGOs. The government of Pakistan is aware of our concerns in this context."
Lashkar-e-Taiba was outlawed in 2002 after being blamed for a bloody attack on the Indian parliament which brought nuclear-armed India and Pakistan close to a fourth war.
It has since re-emerged under the name Jamat-ud-Daawa and has been carrying out high-profile relief work in earthquake-devastated Pakistani-administered Kashmir. The US has also been playing a major role in the rescue effort.
Jamat-ud-Daawa is on the Pakistan government's watchlist of terrorist organisations but is not formally banned.