Pakistan was not warned about a suspected US missile strike in the north-west on Wednesday, Foreign Minister Shah Mahmood Qureshi has said.
Officials say at least five people were killed when a US drone fired missiles at a suspected militant target.
The air strike happened in South Waziristan, close to the Afghan border.
The incident came as the top US military commander met Pakistani officials to discuss growing tension over US attacks along the border.
Observers say Wednesday's attack may be an indication that the Americans have told Pakistan there will be no more ground assaults, but that drone attacks are to continue.
Chairman of the Joint US Chiefs of Staff, Admiral Michael Mullen, met Prime Minister Yousuf Raza Gilani on Wednesday to discuss "measures to defuse tension between the two countries, following a spate of air and ground violations along the Pakistan-Afghan border", the state news agency APP said.
Adm Mullen "reiterated the US commitment to respect Pakistan's sovereignty and to develop further US-Pakistani co-operation... on critical issues that challenge the security and well-being of the people of both countries", the US embassy in Islamabad said afterwards.
'Counter-productive'
Mr Qureshi said on Thursday that such assurances combined with the suspected missile strike indicated "an institutional disconnect" on the US side.
"We were not informed," Mr Qureshi said, after meeting Adm Mullen in Islamabad.
"My understanding of the rules of engagement is that no foreign troops will be permitted to operate in Pakistan," Mr Qureshi 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 - rather they will deteriorate it and will be counter-productive."
Pakistani Prime Minister Yousuf Raza Gilani has also strongly condemned the attacks and is expected to make a statement on them later on Thursday.
Pakistan's army has repeatedly said it will not tolerate cross border incursions from Afghanistan as tension in recent months has risen over an increase in US attacks in the area.
'Secret' order
The missiles in the attack are reported to have struck a militant training camp.
At least six people were injured as well as the five who died, officials told the BBC.
They said four missiles were fired at the village of Baghar Cheena, about half a kilometre from the Afghan border in the tribal region of South Waziristan.
Two reportedly hit a house occupied by militants while two struck the hillside.
Baghar Cheena is about 4km (2.5 miles) from Angoor Adda, a village which Pakistani officials say was the scene of an unprecedented US ground assault earlier this month.
That sparked diplomatic fury from the Pakistani side.
South Waziristan is one of the main areas from which Islamist militants launch attacks into Afghanistan.
Last week, it emerged in Washington that President George Bush had authorised cross-border attacks by US troops based in Afghanistan.
Pakistan's army has warned that the aggressive US policy will widen the insurgency by uniting the tribesmen with the Taleban.
(BBC)
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