A U.S. commando operation inside Pakistan last week, followed by several attacks from drones, has sent tensions soaring between Islamabad and Washington over how to tackle the Taliban and al Qaeda on the Pakistani side of the border with Afghanistan.
Gilani said Pakistan would raise the issue with the United States at diplomatic level.
"We will try to convince the United States ... to respect (the) sovereignty of Pakistan -- and God willing, we will convince," he told reporters.
Security officials said about 12 people were wounded in the attack near the town of Miranshah in North Waziristan. Residents said the pilotless aircraft fired two missiles at a former government school where militants and their families were living.
"We confirm a missile attack at around 5.30 in the morning (2330 GMT on Thursday) ... We have informed the government," said military spokesman Major Murad Khan.
The military, apparently reluctant to highlight infringements of sovereignty, has rarely confirmed such attacks.
Security forces stepped up offensives in two areas in August, the Bajaur region on the Afghan border and the Swat Valley in North West Frontier Province.
The security forces killed 40 militants, including foreigners, in clashes in Bajaur on Friday, raising the death toll to around 150 in fighting this week. Two soldiers were also killed and 16 wounded.
Hours after Friday's missile strike, a roadside bomb hit a security convoy in a nearby village, seriously wounding two soldiers. Soldiers in the convoy opened fire after the blast, wounding four civilians, residents said.
REVISE STRATEGY
Fears about Afghanistan's future and frustration with Pakistani efforts to tackle the militants have led to more U.S. missile attacks by drone aircraft in Pakistan.
About a dozen strikes this year have killed scores of militants and some civilians.
In addition, helicopter-borne U.S. commandos carried out a ground assault in South Waziristan last week, the first known incursion by U.S. troops into Pakistan since the 2001 invasion of Afghanistan.
Pakistan condemned the raid in which officials said 20 people, including women and children, were killed.
Pakistani army chief General Ashfaq Kayani said in a strongly worded statement that Pakistan would not allow foreign troops onto its soil and Pakistan's sovereignty and territorial integrity would be defended at all cost. Kayani also dismissed speculation of a secret deal allowing U.S. forces to attack.
The New York Times reported on Thursday that President George W. Bush had secretly approved orders in July that for the first time allowed U.S. special forces to carry out ground assaults inside Pakistan without the approval of the Islamabad government.
U.S. officials declined to comment on the report and Pakistan's U.S. ambassador Husain Haqqani told Reuters Bush had issued no new orders.
Kayani ended a meeting with his top commanders on Friday saying the military, under government leadership, would protect Pakistan's territory and there was "complete unanimity of views between the government and the army" on the issue.
Tension with the United States has added to the worries of investors who have seen Pakistan's financial markets battered by political turmoil and economic problems.
At the same time, Pakistan is highly vulnerable to any reduction in U.S. financial support given the depletion of its foreign reserves, which has sparked talk it could default on a sovereign bond next year unless it gets foreign financing.
