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Reporting from Islamabad, Pakistan — Lashkar-e-Taiba, the self-styled “Army of the Pure,” has left its footprints in the snows of Kashmir, the back alleys of Lahore and Karachi, the harsh terrain along the Pakistan-Afghanistan frontier — and now, investigators say, in Mumbai, India, the scene of last week’s horrific rampage by gunmen.

The growing case against the Pakistan-based militant organization speaks directly to a doubt that has plagued U.S.-Pakistani relations since the two countries became allies after the Sept. 11 attacks: whether present or former officials in Pakistan’s powerful security establishment continue to nurture radical Islamic groups.

Pakistan’s relatively weak civilian government, in power less than a year, has shown a degree of reluctance to forcefully confront militant groups or to assert control over the intelligence establishment — a pattern that could bode ill as fallout from the attacks on India’s financial capital poisons relations between the two nuclear-armed countries.

Lashkar-e-Taiba’s alleged social wing, which gained prominence after Lashkar was officially banned in 2002, operates openly on a sprawling campus outside the eastern Pakistani city of Lahore. Its head, Hafiz Saeed, was one of the founders of Lashkar and is on a list of about 20 militant suspects India has demanded be handed over.

Pakistan’s government vehemently denies involvement in the Mumbai attacks, which left more than 170 people dead and 300 injured, and U.S. officials say no formal links between the attackers and Pakistani officialdom have been found.

However, Secretary of State Condoleezza Rice told Pakistani officials during a visit Thursday that the evidence gathered so far by Indian and Western investigators against Pakistan-based militants was compelling enough that Islamabad should be acting on it.

Successive Pakistani governments have tolerated and abetted Lashkar-e-Taiba, which for much of its two-decade history was used by Pakistan’s intelligence service as a proxy for fighting Indian rule in the disputed Himalayan territory of Kashmir.

Pakistani officials insist that in recent years the country’s premier spy agency, the Directorate of Inter-Services Intelligence or ISI, has been purged of militant sympathizers. But as recently as four months ago, U.S. intelligence officials alleged that the ISI aided militants who struck another Indian target, its embassy in the Afghan capital, Kabul.

“You could argue that if you have 20 years of active sponsorship, it takes time for these linkages to disappear from the state apparatus,” said Ishtiaq Ahmad, a professor of international relations at Quaid-i-Azam University in Islamabad.

Pakistani President Asif Ali Zardari assured Rice that he would take “strong action” against anyone in Pakistan found to have taken part in the Mumbai attacks. But the government has largely brushed aside investigators’ allegations — some gleaned from the confessions of the sole suspect captured, some from Western intelligence — that the assailants trained at Lashkar-e-Taiba camps in Pakistan, began their sea journey from the Pakistani port of Karachi and conferred with Pakistani handlers in the midst of the assault.

Indian officials, who are being assisted in their investigation by Scotland Yard and the FBI, also say they believe two known Lashkar-e-Taiba commanders masterminded the attack. Pakistani politicians from across the spectrum say India is motivated in its allegations by the long standing enmity between the neighbors.

Lashkar-e-Taiba has maintained an unbroken presence in Pakistan since about 1990 — sometimes operating clandestinely, and sometimes brazenly. Its most visible presence is through Jamaat ud-Dawa, the self-described political and religious movement that U.S. officials believe maintains active ties with Lashkar.

On Thursday, Jamaat took journalists on a tour of its extensive complex in Muridke, outside Lahore. Followers showed off classrooms and dormitories, though they did not allow photos. They insisted that the group is an educational and charitable institution and nothing more. A spokesman, Abdullah Muntazir, told reporters that there was “no link” to Lashkar-e-Taiba.

Saeed, speaking to Pakistan’s GEO television this week, declared that he was not involved in militant activity. But he has never disowned the Islamist beliefs he regularly espouses in fiery sermons.

Pakistan has indicated that it will not comply with India’s demand to extradite the 63-year-old former professor.

The investigation of the Mumbai attacks is complicated, analysts say, by the fact that much of Lashkar-e-Taiba’s operational capability has migrated from the Pakistan-controlled slice of Kashmir to the lawless tribal areas along the border with Afghanistan, where many of its camps and training centers are now believed to be.

Tariq Naqash, a journalist in Muzaffarabad, the capital of Pakistani Kashmir, says the group has dramatically lowered its profile in the area.

“You don’t hear their name these days,” said Naqash, who has written extensively about Lashkar-e-Taiba.

Even the Jamaat, which provided extensive relief aid in Pakistani Kashmir after a devastating earthquake in 2005, largely disappeared from view after a dispute with locals last summer, Naqash said.

Analysts say Lashkar began fragmenting, and to some extent reinventing itself, after Pakistan and India agreed to a Kashmir border truce in late 2003, which stemmed guerrilla infiltration of the Indian side. Feeling that the Kashmiri jihad had lost its momentum with Pakistani peace overtures to India, some adherents, while maintaining ties to Lashkar-e-Taiba, turned their attention to global jihad.

“The tribal belt has attracted a lot of militants who were shunted out of their own organizations, or left in the cold, as they saw it,” said Talat Hussain, a prominent Pakistani television journalist.

Many longtime observers of the group say that although the Mumbai attackers’ military prowess and pinpoint coordination are hallmarks of Lashkar-e-Taiba, the group in all likelihood did not act alone. In recent years, evidence has emerged, according to current and former U.S. and allied counter-terrorism officials, that the group has been working more closely with Al Qaeda and other extremist groups.

“In my opinion, this is an Al Qaeda-planned attack using local surrogates in order to relieve pressure on them in [the tribal areas],” said Ahmed Rashid, a Lahore-based author who writes about Pakistani militant groups. “What better way to do that than create a conflict between India and Pakistan?”

The Kashmir struggle left Pakistani groups well-schooled for carrying out attacks like those in Mumbai, Rashid said.

“They were well-versed in urban surveillance and urban terrorism — these are not Pashtun tribesmen and mullahs,” he said. “These were well-trained, sophisticated guys with 15 years of battle experience.”

Indian investigators have said that the captured suspect told them that at least one former Pakistani military officer took part in training the gunmen — a credible scenario, in the view of some observers.

“Some handlers of these organizations, intelligence officials, didn’t wear a uniform,” said Hassan Abbas, a former Pakistani law enforcement official who is a research fellow at Harvard University’s Belfer Center. “Even if they’ve been thrown out of their agency, their clients might not know; they meet in a small mountain town, and their clients don’t really know whether they are current or former ISI.”

But even if the attack is tied indirectly to the ISI, the main thrust at the agency’s top levels appears to be to disassociate itself from militant activity, in an attempt to rehabilitate its tarnished image.

“I’m not sure it’s become a moral organization overnight, but when you already have a ‘rogue agency’ label stuck on your forehead, you’re going to be busy trying to rip it off,” said Hussain, the TV journalist.

“They are trying to curry favor with Washington and build an institutional linkage with them,” he said. “So the advantages of being associated with something like this are hugely outweighed by the disadvantages.”

King is a Times staff writer.

laura.king@latimes.com

Special correspondent Anjum Herald Gill in Muridke contributed to this report.