A truck bombing over the weekend at the luxury Marriott hotel in the capital Islamabad that killed 53 people underscored the threat extremists pose to the nuclear-armed nation.
More than 50 of the alleged insurgents, along with one soldier, were killed in clashes since Monday in the Kohat region bordering Pakistan's semiautonomous tribal areas, army spokesman Maj. Murad Khan said.
He said the military had retaken control of a key mountain tunnel from the insurgents.
In the nearby Bajur tribal region, security forces killed at least 10 militants during an ongoing offensive there, government official Iqbal Khattak said.
That operation, which began in early August, has won praise from U.S. officials worried about rising violence in Pakistan and Afghanistan. But it has also triggered retaliatory suicide bombings elsewhere in Pakistan.
Some officials have said the weekend bombing of the American hotel chain may have been a response to the Bajur operations, which the army says has killed more than 700 suspected militants.
Washington says the operation in Bajur - a rumored hiding place of al-Qaida leader Osama bin Laden - appears to have reduced violence across the border in Afghanistan.
Pakistan army spokesman Maj. Gen. Athar Abbas has said Bajur had turned into a "mega-sanctuary" for militants and the military was determined to flush them out.
However, a rash of U.S. cross-border operations in neighboring tribal regions, including suspected missile strikes and a ground assault, underscore Washington's concerns that Pakistan is either unwilling or incapable of rooting out extremists on its own.
Pakistani President Asif Ali Zardari was expected to discuss the cross-border attacks with President Bush on Tuesday on the sidelines of the U.N. General Assembly in New York.
In the latest such alleged breach, two U.S. helicopters crossed one mile into Pakistan late Sunday in the Alwara Mandi area in North Waziristan, two intelligence officials said on condition of anonymity because they were not authorized to speak to the media.
Citing informants in the field, they said Pakistani troops and tribesmen responded with small arms fire, but it was not clear whether the bullets were aimed at the choppers or were warning shots. The helicopters did not return fire and re-entered Afghan airspace without landing, the officials said.
That account was denied by the Pentagon.
"There was no such incursion, there was no such event," said Defense Department spokesman Col. Gary L. Keck.
Pakistan has protested U.S. cross-border operations, calling them violations of its sovereignty. But its government has called for diplomatic measures to resolve the dispute.
Zardari told NBC television in a recent interview that he welcomed U.S. intelligence help, but not its troops.
"Give us the intelligence and we will do the job," he said. "It's better done by our forces than yours."
Experts and officials say the Marriott truck bombing bore the hallmarks of al-Qaida, but that the Taliban may still have assisted in its execution.
Late Monday, Dubai-based TV channel Al-Arabiya said it received a tape from a little known group calling itself "Fedayeen al-Islam" - Arabic for "Islam commandos" - claiming responsibility for the Marriott bombing and calling on Pakistan to end cooperation with the United States.
The U.S. Department of Defense identified one of two Americans killed in the Marriott blast as Maj. Rodolfo I. Rodriguez, 34, of El Paso, Texas. He was assigned to the 86th Construction & Training Squadron, Ramstein Air Base, Germany.
In the northwestern town of Swat, rioters torched bank in a protest against the lack of electricity and gas, said police officer Mohibullah Khan. Police fired warning shots to disperse the rioters. Khan said militants bombed the Swat's electricity station and gas line supplying the town last week.
In Geneva, Switzerland, the U.N. refugee agency is asking for donations of $17 million to aid more than 300,000 people in Pakistan who have fled fighting and floods near the Afghanistan border, an official said Tuesday.
The U.N. High Commissioner for Refugees has already distributed supplies to 84,000 people displaced by floods in northwestern Pakistan, and could provide shelter and other relief to more than three times that number if donations are forthcoming, agency spokesman William Spindler said.
Pakistan's government has estimated that 90,000 people who fled recent fighting remain in North West Frontier Province along the Afghan border and a similar number are displaced in the northern part of the province around Swat, Spindler said.
Associated Press reporter Alexander G. Higgins contributed to this report from Geneva, Switzerland.