Ms Patterson will convey Pakistan's concerns to Washington
Pakistan has summoned the US ambassador in Islamabad to protest at a US missile attack deep inside Pakistani territory on Wednesday that killed five people.
The attack, in Bannu district, killed five local militants, officials say.
The protest comes as a top Taleban commander says he will pull out of a peace deal with Pakistan's military if there are more US missile strikes.
Hafiz Gul Bahadur, the main commander in North Waziristan, has been at peace with the army since 2006.
There is widespread anger and resentment in Pakistan at the increasing use of missile strikes by unmanned US drones along the tribal Afghan-Pakistan border.
Wednesday's strike in Bannu was unusual because it hit much further inside Pakistani territory.
Previous drone attacks have been in the strip of territory along the Afghan border known as the Federally Administered Tribal Areas (Fata), a region where huge areas are under the control of militants rather than the central government.
But Bannu is in the North West Frontier Province where the government claims far more control.
"The American ambassador has been called to the Foreign Office to lodge a protest over the missile attack in Bannu," a foreign ministry official told Reuters news agency.
The US embassy said that ambassador Anne Patterson would relay Pakistan's concerns to Washington.
Meanwhile, North Waziristan militant Hafiz Gul Bahadur has demanded an end to the missile strikes. His territory has been the target of several missile strikes by suspected US drones from Afghanistan since August.
A spokesman said his group would carry out attacks outside the tribal areas if there were any new US attacks.
Waziristan on the Afghan border is believed to be a safe haven for the Taleban and al-Qaeda militants.
The US says the insurgents use the territory to launch attacks against coalition forces in Afghanistan.
Since August, the territory of Bahadur and his compatriot Mullah Nazir has been hit 19 times by missiles fired by suspected US drones.
"Our council of leaders met under Hafiz Gul Bahadur on Wednesday," Ahmedullah Ahmedi, spokesman for Bahadur's militia, told the BBC.
"It has been decided that if there are any drone attacks in our territory after 20 November, we will attack targets in Pakistani territory outside the tribal areas," he said.
The government has been pursuing a policy of ad-hoc peace deals with local Taleban commanders.
"Pakistan is directly involved in aiding America to carry out these attacks," Mr Ahmedi said.
He said the US could not attack any of the targeted areas without help from Pakistan.
The Taleban have a huge presence in Pakistan's tribal areas
"American and Pakistani claims that foreigners have died in the attacks are false," he said.
"Only local militants and civilians have been killed in the missile attacks."
Pakistan has three major Taleban factions led by Mullah Nazir, Hafiz Gul Bahadur and Baitullah Mehsud.
Insiders say the militant groups in Bajaur and Swat draw their strength from Baitullah Mehsud's faction, which has been in open conflict with Pakistani security forces.
Both Mullah Nazir and Hafiz Gul Bahadur have avoided conflict with the government and kept a low profile.
In March 2007, Mullah Nazir helped the Pakistan army chase Uzbeks belonging to the al-Qaeda affiliated Islamic Movement of Uzbekistan out of Waziristan.
Hafiz Gul Bahadur - who returned to Pakistan in late 2007 after a year-long spell in Afghanistan fighting the US-led coalition - broke away from the Baitullah Mehsud-led Tehrik-e-Taleban organisation once it openly declared hostilities with the Pakistan army.
But the BBC's Syed Shoaib Hasan in Islamabad says relations between both Bahadur and Mullah Nazir's factions and the Pakistan government have deteriorated since the missile strikes started in August.
Both the commanders had refrained from conflict with Pakistani security forces.
The drone attacks have led to a change of heart in both factions. Mullah Nazir's men are reported to have been two attacks in Waziristan.
Security experts now fear that a new and far deadlier round of suicide attacks could be around the corner, our correspondent says.
In a separate development, the Nato-led peacekeeping force in Afghanistan, Isaf, said it had worked in co-ordination with Pakistani forces to target insurgents in Pakistan in an incident on Thursday.
Isaf said the insurgents fired rockets and hit an Isaf outpost and a border checkpoint in Paktika province.
Isaf said in a statement that it then "contacted the Pakistani military for support. The Pakistani military then launched a mortar strike on the insurgents' firing location inside Pakistan".
It said there were no reports of Isaf or Pakistani casualties.