Ben Emmerson, the UN special rapporteur for protecting human rights and fundamental freedoms while countering terrorism, said the Pakistan government had informed him that it does not consent to the strikes.
He said Pakistani officials had confirmed some 400 civilian deaths in drone attacks.
Imtiaz Gul, a Pakistani analyst and author who helped Emmerson's team, told the media that he had given 25 instances of drone strikes that allegedly killed civilians.
Pakistan's Foreign Office confirmed Emmerson's visit during March 11-13 in a statement issued this evening.
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Emmerson met Foreign Minister Hina Rabbani Khar, the Advisor to the Prime Minister on Human Rights, the head of the Senate Standing Committee on Defence, the Foreign Secretary and senior government officials.
"In order to ascertain first-hand information on drone strikes and its impact on civilians, the Special Rapporteur also met tribal Maliks and victims of drone strikes in Islamabad," the statement said.
Emmerson said that the drone campaign "involves the use of force on the territory of another state without its consent and is therefore a violation of Pakistan's sovereignty".
Emmerson is expected to present his final report on drones during the next session of the General Assembly in October.
President Barack Obama has stepped up CIA drone strikes targeting Al Qaida and Taliban elements in Pakistan's lawless tribal region since 2009.
The strikes have triggered anger among Pakistanis because of the secrecy surrounding them and claims that they have caused significant civilian casualties.
US officials have also disputed claims that the strikes have killed a large number of civilians.
For a long time, Pakistan allowed US drones to operate from bases within the country.
In 2011, Pakistan forced US military personnel to vacate an airbase used by drones in the southwestern Balochistan province.