Pakistan’s powerful intelligence agency not only funds and trains Taliban insurgents fighting U.S. and NATO troops in Afghanistan, but also maintains its own representation on the insurgency’s leadership council, claims a new report issued by the London School of Economics.

Assertions that Pakistan’s intelligence agency, the Inter-Services Intelligence, continues to nurture links with the Afghan Taliban are not new. But the scope of that relationship claimed by the report’s author, Matt Waldman, is startling and could prove damaging to the fragile alliance Washington is trying to foster with Pakistan, its military establishment, and its weak civilian government led by President Asif Ali Zardari.

Waldman, a fellow at the Kennedy School of Government at Harvard University, based his assertions on interviews with nine Afghan Taliban commanders as well as with Afghan and Western security officials. The report claims that it is official Pakistan governmental policy to support the Taliban’s insurgency in Afghanistan, and that the ISI has a strong voice on the Quetta shura, the Afghan Taliban’s leadership council, named after the southern Pakistani city believed to serve as the council’s haven.

The report states that, based on the interviews, “the ISI has representatives on the Shura, either as participants or observers, and the agency is thus involved at the highest level of the movement.”

The report also alleges that Zardari, long regarded as a close ally of the Obama administration in the war on terrorism, had met with captured senior Taliban leaders in Pakistan and had vowed to ensure their release as well as to support their efforts in Afghanistan.

The report’s claims drew vehement denials from Islamabad, which characterized the research as speculative and unsubstantiated.

“I consider this a highly speculative and provocative report,” said Pakistani military spokesman Maj. Gen. Athar Abbas. “I question the authenticity and credibility of this so-called research. … It’s not worthy of any response.”

Pakistan’s links to the Afghan Taliban have been among the thorniest issues complicating the U.S.-Pakistan relationship and the ongoing effort to uproot Al Qaeda and other Islamic extremist organizations in the region. Though Islamabad insists that it does not support Taliban insurgents battling Afghan President Hamid Karzai’s government and Western troops, U.S. diplomats and military commanders have long suspected that Pakistani officials, particularly in the intelligence community, have never severed ties with the Afghan Taliban.

Many observers maintain that Pakistan continues to support the Afghan Taliban behind the scenes as a way of countering attempts by its nuclear archrival, India, to expand influence within Afghanistan and with the Karzai-led government.

Earlier this year, Pakistan arrested several high-ranking Taliban leaders that had sought refuge in Karachi and other Pakistani cities, including the insurgency’s second-in-command, Mullah Abdul Ghani Baradar. However, analysts suggested that the arrests, which were welcomed by the U.S., may have been aimed at ensuring Pakistan’s seat at the negotiating table whenever the West, Karzai and the Taliban embarked on peace talks.

Pakistan’s calibrated approach toward dealing with the Taliban is especially evident in the country’s largely lawless tribal areas along the Afghan border. There the Pakistani military aggressively pursues Taliban insurgents that have targeted security installations and civilians, but insurgents that focus principally on Afghanistan, such as the Haqqani network in North Waziristan, are left alone.

Appearing on Al Jazeera television, Waldman defended his research, saying that in addition to speaking to Afghan Taliban field commanders, he spoke to several officials from Western governments who concurred with his findings.

“These are not erratic allegations,” Waldman said. “They’re not without foundation, without a lot of support from analysts around the world.”

alex.rodriguez@latimes.com