Orders President Bush signed in July authorizing raids by special operations forces in the areas of Pakistan controlled by the Taliban and Al Qaeda and undertaking those raids without official Pakistani consent, have roots stretching back to the days following the 9/11 terrorist attacks.

In an address to a joint session of Congress nine days after 9/11, President Bush said, "From this day forward any nation that continues to harbor or support terrorism will be regarded by the United States as a hostile regime."

But even before that declaration, two key steps had been taken: One, Congress had authorized the use of US military force against terrorist organizations and the countries that harbor or support them. Two, Bush administration officials had warned Pakistan's leaders of the dire consequences their country would face if they did not unequivocally enlist in the fight against radical Islamist terrorism.

What Mr. Bush's July orders signify is that, after seven years of encouraging Pakistan to take on extremists harbored in remote areas along its border with Afghanistan and subsidizing the Pakistani military handsomely to do it, the US has become convinced that Pakistan is neither able nor willing to fight the entrenched Taliban and Al Qaeda elements. Indeed, recent events appear to have convinced at least some in the administration that parts of Pakistan's military and powerful intelligence service are actually aiding the extremists.

"We've moved beyond the message stage here. I think the US has had it with messages that don't get any action, and that is why the president authorized this," says Kamran Bokhari, director of Middle East analysis for Stratfor, an intelligence consulting firm in Washington. "This says loud and clear, 'We're fed up.' "

Even before the July order, the US had undertaken covert operations in Pakistan's tribal areas. Moreover, the CIA over the past year has stepped up missile attacks by the unmanned Predator drones it operates to hit targets in the region. That increase has coincided with a deterioration of the war in Afghanistan, where the Afghan Army and NATO forces have come under increasing attack from militants crossing over the rugged and lawless border from Pakistan.

But Bush's orders, first reported in The New York Times Thursday, mean that operations against insurgent sanctuaries will become overt and probably more frequent. A Sept. 3 ground assault involving US commandos dropped from helicopters targeted a suspected terrorist compound. Missile attacks by the CIA's unmanned drones, including one Friday reported by Pakistani officials to have killed at last 12 people, are also on the rise.

Precedence for the orders authorizing the attacks on terrorist havens can be found in President Bill Clinton's authorization of retaliatory attacks in 1993 (against Iraqi intelligence facilities) and in 1998 (against terrorist camps in Afghanistan and Sudan), and in President Ronald Reagan's bombing of Libya, legal scholars say.

The administration has debated the use of commando raids in Pakistan for years, but the tipping point came in July, as relations with Pakistan's civilian and military leaders deteriorated, intelligence sources say. The "kicker," according to one source who requested anonymity over the sensitivity of the issue, was two July events: the bombing of India's embassy in Afghanistan's capital, Kabul, an act that US intelligence officials concluded was aided by Pakistani intelligence operatives; and a July 13 attack on a US military outpost in eastern Afghanistan that killed nine US soldiers. The outpost attack was carried out by Taliban militants who had crossed over the nearby border from Pakistan.

The evolution of operations in Pakistan from covert to overt actions is reminiscent of a trajectory followed in some aspects by the Vietnam War, some analysts note.

Patrick Lang, a former Middle East analyst for the Defense Intelligence Agency, says the evolution in Pakistan is similar to what occurred in Cambodia during the Vietnam War, when US operations against Vietcong sanctuaries there were initially covered up.

"We initially crossed into Cambodia as covert forces, but that changed," says Mr. Lang, who was part of special forces that carried out the Cambodia operations. By 1970, cross-border operations against enemy sanctuaries were being carried out in the open. Looking at the evolution in operations in Pakistan, the national security analyst says, "We are letting [Pakistanis] know this could evolve into bigger things."

Adds the intelligence source who requested anonymity, "The message is to the new civilian leadership and the military, 'We have bought all these toys for you – if you don't use them and do things in these areas that are causing us problems, we'll do them for you.' "

The new orders reflect flagging confidence in Pakistan's civilian and military leadership to address the problem of the Taliban and terrorist havens, which are thought to harbor Al Qaeda leader Osama bin Laden and his deputy, Ayman al-Zawahiri. For seven years the Bush administration focused its Pakistan policy on President Pervez Musharraf and his assurances that he was battling the militant sanctuaries. But Mr. Musharraf was forced to resign last month after suffering a crushing electoral defeat earlier in the year, and the US appears to have little confidence in the new civilian and military leaders.

"Musharraf was a one-stop shopping center for US relations with Pakistan, but that no longer exists," says Stratfor's Mr. Bokhari. Senior State Department officials have met with Pakistan's new civilian leaders, he notes, while top Pentagon officials have met with the military leadership including Army chief of staff Gen. Ashraf Parvez Kayani, the top military commander.

"The sense I get is they were given the runaround, and they came away from all these meetings convinced the leadership structure has become much more complex at a time when the Taliban are becoming stronger and the situation in Afghanistan is deteriorating," Bokhari says. "The feeling was the US couldn't sit by and see how the leadership sorts itself out."

Bush's orders authorizing cross-border incursions into Pakistan mean in a sense that the rules governing US special operations have shifted from yellow to green. The military will no longer need a presidential "finding" for each operation – and that, military analysts say, means the handling of forays into Pakistan will fall increasingly into military rather than CIA hands.

That has some intelligence officials worried that the consequences of stepped-up US operations in Pakistan – in terms of Pakistani public opinion and the stability of the government – will get short shrift. According to intelligence sources, officials from the National Intelligence Council recently briefed the Bush administration's national security team on the potentially dire consequences of US actions that could destabilize the government of a country with nuclear weapons.