Pakistan says the US failed to warn it about a suspected missile attack carried out while a senior US official was in the country assuring leaders that Washington would respect their sovereignty.
Five people were killed when unmanned drones fired missiles into a village in Pakistan's South Waziristan on Wednesday evening, according to Pakistani officials.
"We were not informed," Shah Mahmood Qureshi, Pakistan's foreign minister, said at a news conference on Thursday.
"My understanding of the rules of engagement is that no foreign troops will be permitted to operate in Pakistan," he said.
"If there is action required inside our territory, it will be carried out by our forces.
"Our stance is that we should co-operate with each other, and such incursions cannot improve the atmosphere, and rather they will deteriorate it, and will be counterproductive," he said.
Admiral Mike Mullen, chairman of the US joint chiefs of staff, met Qureshi as well as other Pakistani officials, including the prime minister, on Wednesday.
"Our stance is that we should co-operate with each other, and such incursions cannot improve the atmosphere"
Shah Mahmood Qureshi
Pakistan foreign minister
A US embassy statement said that Mullen wanted to "develop further US-Pakistani co-operation and co-ordination on these critical issues that challenge the security and well-being of the people of both countries".
"The conversations were extremely frank, positive, and constructive," the US embassy said.
Sources said Pakistani officials told Mullen that unilateral cross-border raids by US ground forces based in Afghanistan would not deal a blow to al-Qaeda and the Taliban.
"Such raids will be a setback to our efforts against the militants' network," an official, speaking on condition of anonymity, told AFP news agency.
Intelligence officials told The Associated Press news agency that several missiles hit a compound in South Waziristan used by pro-Taliban fighters and Hezb-i-Islami, another group purportedly involved in attacks on US and government troops in neighbouring Afghanistan.
Another Pakistani official told the Reuters news agency that the raid was the result of intelligence sharing between Pakistan and the US.
Gonzalo Gallegos, a spokesman for the US embassy, declined to comment on the reports.
Wednesday's reported attack took place in Baghar, a village in the mountains 55km west of Wana, the main town in the region, close to Angor Adda, the border village that was raided by US commandos on September 3.
Several media reports have quoted officials and other sources as saying that that raid was approved without the consent of Islamabad under a presidential order on covert operations signed by George Bush, the US president.
US officials say that armed fighters are using the tribal areas in northwestern Pakistan as a base to launch attacks on Afghan and US forces operating across the border, but six missile strikes by pilotless drones and the commando raid have angered Pakistanis.