Pakistan's Prime Minister Yousuf Raza Gilani said US drone strikes targeting Al-Qaeda and Taliban militants were counter productive and his country had not given permission for such attacks.
"First of all I want to inform you that we did not allow or give permission to fly drones from Pakistan," Gilani told Al Jazeera television in an interview broadcast Saturday.
"Drones are counter productive and we have discussed it thoroughly with the US administration."
Gilani said the "collateral damage" from drone attacks was counter productive because it undermined his government's efforts to separate tribes from militants, and also violated Pakistan's sovereignty.
Gilani said Pakistan's former military ruler Pervez Musharraf had "some understanding" on drone attacks with the United States.
US diplomatic cables leaked by WikiLeaks in late 2010 showed Pakistan's civilian and military leaders privately supported US drone attacks, despite public condemnation in a country where the US alliance is hugely unpopular.
The United States had until now refused to discuss the strikes publicly, but the programme has dramatically increased as the Obama administration looks to withdraw all foreign combat troops from Afghanistan by the end of 2014.
Obama only confirmed the secret drone programme in late January this year.
US missiles on Thursday killed the most senior Pakistani in Al-Qaeda and one of the main US targets in the country.
Badar Mansoor, who reputedly sent fighters to Afghanistan and ran a training camp in North Waziristan, was killed in a drone strike near the Afghan border, Pakistani officials and a member of his group told AFP.
According to an AFP tally, 45 US missile strikes were reported in Pakistan's tribal belt in 2009, 101 in 2010 and 64 in 2011.
Islamabad is reviewing its alliance with the United States and has kept its Afghan border closed to Nato supply convoys since November air strikes which killed 24 soldiers.
When the route eventually re-opens, it is widely expected to tax NATO convoys carrying supplies shipped to its port in Karachi and trucked through its territory to landlocked Afghanistan.
The United States has made increasing use of alternative routes into Afghanistan through the north in order to mitigate against losses in Pakistan.