The orders, which come in response to a highly unusual Sept. 3 ground attack by U.S. commandos, are certain to heighten tensions between Washington and a key ally against terrorism. Although the ground attack was rare, there have been repeated reports of U.S. drone aircraft striking militant targets, most recently on Sept. 12.
However, the Pentagon said Islamabad will "correct the record" the volatile statement.
Spokesman Bryan Whitman said Pakistan is an ally in the global war on terror, adding that the U.S. enjoys "good cooperation with Pakistan along the border."
Pakistani officials warn that stepped-up cross-border raids will accomplish little while fueling violent religious extremism in nuclear-armed Pakistan. Some complain that the country is a scapegoat for the failure to stabilize Afghanistan.
Pakistan's civilian leaders, who have taken a hard line against Islamic militants since forcing Pervez Musharraf to resign as president last month, have insisted that Pakistan must resolve the dispute with Washington through diplomatic channels.
However, army spokesman Maj. Gen. Athar Abbas told The Associated Press that after U.S. helicopters ferried troops into a militant stronghold in the South Waziristan tribal region, the military told field commanders to prevent any similar raids.
"The orders are clear," Abbas said in an interview. "In case it happens again in this form, that there is a very significant detection, which is very definite, no ambiguity, across the border, on ground or in the air: open fire."
U.S. military commanders accuse Islamabad of doing too little to prevent the Taliban and other militant groups from recruiting, training and resupplying in Pakistan's wild tribal belt.
Pakistan acknowledges the presence of al Qaeda fugitives and its difficulties in preventing militants from seeping through the mountainous border into Afghanistan.
However, it insists it is doing what it can and paying a heavy price, pointing to its deployment of more then 100,000 troops in its increasingly restive northwest and a wave of suicide bombings across the country.
After talks Tuesday with British officials in London, Pakistani President Asif Ali Zardari said he did not "think there will be any more" cross-border raids by the U.S. He declined to comment on the order to use lethal force against American troops.
Instead, he and British Prime Minister Gordon Brown issued a joint statement saying Afghanistan and Pakistan should lead the efforts to battle border militancy. The joint statement left out any mention of the United States.
American officials have confirmed their forces carried out the Sept. 3 raid near the town of Angoor Ada but given few details of what happened.
Abbas said that Pakistan's military had asked for an explanation but received only a "half-page" of "very vague" information that failed to identify the intended target.
Pakistani officials have said the raid killed about 15 people, and Abbas said they all appeared to be civilians.
"These were truck drivers, local traders and their families," he said.
How to reverse a surge in Taliban violence in Afghanistan has become a major issue in the U.S. presidential campaign and refocused attention on the porous border with Pakistan.
Pakistan's military has won American praise for a six-week offensive against militants in the Bajur tribal region that officials here say has killed 700 suspected insurgents and about 40 troops. Troops backed by warplanes killed eight more alleged militants Tuesday, officials said.
In the same timeframe, there has been a surge in missile strikes apparently carried out by unmanned U.S. drones. Such attacks killed at least two senior al Qaeda commanders earlier this year.
Abbas did not say when exactly the orders for Pakistani troops to open fire to prevent cross-border raids by U.S. troops were issued. He wouldn't discuss whether Gen. Ashfaq Parvez Kayani, who replaced Musharraf as army chief last year, personally took the decision or if the orders had been discussed with American officials.
The spokesman also played down suggestions that the instructions had been put into practice before dawn on Monday, when U.S. helicopters reportedly landed near Angoor Ada only to fly away after troops fired warning shots.
Abbas insisted no foreign troops had crossed the border and that "trigger-happy tribesmen" had fired the shots. Pakistani troops based nearby fired flares to see what was going on, he said.
The U.S. military in Afghanistan said none of its troops were involved.
In a rare public statement last week, Kayani said Pakistan's sovereignty would be defended "at all cost." Abbas said Pakistani officials had to consider public opinion, which is skeptical of American goals in the region and harbors sympathy for rebels fighting in the name of Islam.
"Please look at the public reaction to this kind of adventure or incursion," Abbas said. "The army is also an extension of the public and you can only satisfy the public when you match your words with your actions."
Meanwhile, U.S. lawmakers are promising close scrutiny of the Bush administration's request to divert hundreds of millions of dollars in anti-terrorism aid to upgrade Pakistan's aging fleet of U.S.-made F-16 fighter planes.
The Bush administration says the upgraded F-16s will allow Pakistan to better conduct precision attacks on terrorists. But the planes have not traditionally been used in anti-terrorism operations. Pakistan sees them as an asset in its arms race against rival India.