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A new report heightens suspicion that Osama bin Laden may have been protected on behalf of, or at least with the knowledge of, Pakistan's intelligence agency.

The cellphone of bin Laden's courier, seized in the US raid on his Abbottabad compound last month, contained contacts for commanders in a militant group with close ties to Pakistan's Inter-Services Intelligence (ISI), The New York Times reported today.

By tracing calls made with the courier's phone, American analysts deduced that commanders from the Harakat-ul-Mujahedeen militant group were in contact with Pakistani intelligence, US officials told the Times – though how they deduced that is unclear.

Harakat, which is particularly entrenched around Abbottabad, was set up with the ISI's blessing at least 20 years ago and has since been mentored by the spy agency. The implication is that if a group so close to the ISI was in touch with bin Laden's network, it is less likely that the spy agency could have been unaware of the terrorist leader's activities in Pakistan.

The US officials were quick to say, however, that there is no proof that the communication was about bin Laden, making it possible that the ISI was unaware of the terrorist leader's presence – although two former militant leaders interviewed by the Times say they are convinced the ISI was protecting bin Laden.

A Pakistani security official told CBS News that the links between the ISI and Harakat no longer existed. "This is outdated information about Harakat-ul-Mujahadeen. Since militant groups began attacking the state [of Pakistan] lots of previous ties have been broken off," he said.

The ISI has long kept ties with Pakistani militant groups for a variety of reasons, including access to intelligence on militants and the desire for more allies against arch-rival India.

"We know the Pakistanis have sponsored some of these groups for a long time," a Western diplomat in Islamabad told [CBS reporter] Bokhari. "Whether there were active contacts between the ISI and these militant groups while they (militant groups) were in touch with OBL needs to be carefully examined. Proving this triangular relationship is not easy."

US officials continue to express doubts that bin Laden could have lived for years in a Pakistani garrison city of nearly 1 million residents only a couple hours from Islamabad without Pakistani officials at least suspecting he was there. American suspicions of Pakistani complicity, together with the unilateral nature of its raid on bin Laden's compound, have dragged down US-Pakistan relations.

According to Bloomberg, 69 percent of Pakistanis see the US as more of an enemy than a partner, despite massive US aid to the country that extends beyond military and counterterrorism assistance.

Even so, Pakistan's need for economic aid, status as a nuclear power, vulnerability to militants and interests in Afghanistan provide incentives for both nations to work through current disputes. "This is a long-term, frustrating, frankly sometimes very outraging kind of experience," Secretary of State Hillary Clinton said about dealing with Pakistan in an appearance before the Senate Foreign Relations committee yesterday. "And yet, I don't see any alternative, if you look at vital American national interests."

According to the Times, discovering the link to Harakat answers a lot of basic questions about how bin Laden ended up in Abbottabad and how he could remain there safely for so long. The group has "deep roots" around the town and an extensive network in the country, which includes ties to both Al Qaeda and ISI. The fact that they are native Pakistanis gives them more freedom of movement than Al Qaeda's foreign militants.

Harakat is one of a host of militant groups set up in the 1980s and early ’90s with the approval and assistance of Pakistan’s premier spy agency, the Directorate for Inter-Services Intelligence, or ISI, to fight as proxies in Afghanistan, initially against the Soviets, or against India in the disputed territory of Kashmir. Like many groups, it has splintered and renamed itself over the years, and because of their overlapping nature, other groups could have been involved in supporting Bin Laden, too, officials and analysts said. But Harakat, they said, has been a favored tool of the ISI. Harakat “is one of the oldest and closest allies of Al Qaeda, and they are very, very close to the ISI,” said Bruce O. Riedel, a former Central Intelligence Agency officer and the author of “Deadly Embrace: Pakistan, America, and the Future of the Global Jihad.”

Separately, US officials disclosed that one of the letters obtained from the bin Laden compound reveals that bin Laden thought Al Qaeda had an image problem. He wanted to rebrand the terrorist group by giving it a new name, the Associated Press reported.

The problem with the name was the lack of religious elements. Without a religious connotation in the name Al Qaeda, the US was able to claim that it was not at war with Islam and it was harder to convince Muslims that they were fighting a holy war, bin Laden reasoned.