The attacks come amid intense U.S. pressure on Pakistan to crack down on militants blamed for attacks both at home and on coalition forces in neighboring Afghanistan.
A truck bombing over the weekend at a luxury 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, died in clashes since Monday in Kohat region, which borders Pakistan's semiautonomous tribal areas, army spokesman Maj. Murad Khan said.
He said the military had retaken control of 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 has triggered retaliatory suicide bombings elsewhere in Pakistan.
Some officials believe the weekend bombing of the Marriott Hotel may have been a response to the Bajur operations, which the army says has left more than 700 suspected militants dead.
Washington says the operation in Bajur - a rumored hiding place of al Qaeda leader Osama bin Laden - appears to have reduced violence across the border in Afghanistan.
Pakistan's 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 U.S. President George W. 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 (two kilometers) 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.The helicopters did not return fire and re-entered Afghan airspace without landing, the officials said.
That account was denied by Pentagon officials.
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.
Meanwhile, at least six people - including a 12-year-old boy - were killed and a bank set on fire in rioting in Mangora in the northwestern Swat valley, police and a hospital official said.
It was unclear how the people died, but police said they fired warning shots to control the mob, who were protesting the lack of electricity and gas to the town.
Police officer Mohibullah Khan said militants bombed Swat's electricity station and gas line supplying the town last week.
In Geneva, Switzerland, the U.N. refugee agency said it was 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.
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 along the Afghan border and a similar number are displaced in the northern part of the province around Swat, Spindler said.
The hotel attack, a favorite spot for foreigners in Islamabad, has led diplomatic missions, aid groups and other expatriate organizations to review security measures.
A spokesman for British Airways on Tuesday said it was "indefinitely" suspending its flights to and from Pakistan "in light of the current security situation."
The company that runs four visa application centers for the British High Commission in Pakistan has closed them pending a security review, commission spokesman Aidan Liddle said.