In this 2010 file photo, an unmanned U.S. Predator drone flies over Kandahar Air Field, southern Afghanistan. (Kirsty Wigglesworth/AP)

CIA drone strikes on targets in Pakistan violate its national sovereignty and have resulted in far more civilian casualties than the U.S. government has recognized, a special U.N. human rights envoy reported after a secret investigation in Pakistan this week.

Ben Emmerson, the United Nations’ special rapporteur on human rights and counter-terrorism, met with Pakistani government officials for three days and came away supporting their long-stated view that they do not consent to the remote-fired missile campaign that is the centerpiece of U.S. strategy to eliminate a wide range of Islamic militants.

This contradicts Washington’s position that the Pakistani military and intelligence services have at least tacitly supported the strikes, which began in 2004 and have significantly escalated since President Obama took office. At one point earlier in the campaign, the two nations shared intelligence on militant targets, but Pakistani officials vehemently deny that they are still doing so.

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 said in a statement released Thursday that only gained wider notice Friday.

State Department spokeswoman Victoria Nuland said that the Obama administration had “seen [Emerson’s] press release,” but would not comment on classified information.

The two countries are allies but their relationship has been plagued by mistrust over the last 50 years.

“What I would say,” she added, “is that we have a strong ongoing counterterrorism dialogue with Pakistan, and that will continue.”

For years the Obama administration has asserted that its covert, targeted killings with unmanned aircraft hovering over Pakistan and elsewhere are proper under U.S. and international law. Targets are chosen under strict criteria and civilian deaths and injuries are rare, the CIA says.

Emmerson, a British lawyer, said Pakistani officials have confirmed that at least 400 civilians had been killed as a result of drone strikes, and that another 200 individuals killed were “probable noncombatants.”

Estimates of total militant deaths and civilian casualties vary widely. Independent confirmation is difficult in part because the strikes often occur in remote, dangerous tribal areas where Taliban insurgents and al-Qaeda and its allied militants are active.

The Bureau of Investigative Journalism in London has estimated that at least 411 civilians – or as many as 884 – were among some 2,536 to 3,577 people killed in the CIA strikes in Pakistan. But Sen. Dianne Feinstein (D), who chaired the Senate Select Committee on Intelligence hearings last month that confirmed new CIA Director John O. Brennan, put the number of civilian deaths considerably lower.

‘The figures we have obtained from the executive branch, which we have done our utmost to verify, confirm that the number of civilian casualties that have resulted from such strikes each year has typically been in the single digits,” she said.

Emmerson conducted talks this week with senior civilian Pakistani officials, as well as representatives of tribal areas where the remotely piloted vehicles operate.

Emmerson reviewed 25 case studies of drone attacks dating to 2005, compiled by a Pakistani research group, and heard from tribal leaders who said innocent residents were targeted simply because their tribal clothing is the same as that worn by Taliban militants. Tribesmen also carry guns at all times, leading to other erroneous targeting, the statement said.

“Adult males carrying out ordinary daily tasks were frequently the victims of such strikes,” Emmerson reported.

Imtiaz Gul, an author who worked on the case studies and is head of the Centre for Research and Security Studies in Islamabad, said although a target may be legitimate, “a legitimate drone strike can kill innocent people.”

He said his research also found that Taliban members bear a significant onus for civilian deaths. Militants are known to demand food and shelter from families against their will – leading to women and children in those homes being killed in a strike.

And militants who know they are being hunted park their cars next to homes of innocent people and then hide a few houses away, so the drone operator ends up targeting the wrong house, Gul said.

During Emmerson’s visit, evidently kept secret for security reasons, he did not meet with the key decision-makers in the drone program over the years: the Pakistan military and the Inter-Services Intelligence spy agency. “However, he was informed that their position would be adequately reflected by consultations with the Ministry of Foreign Affairs, the Ministry of Interior and the Ministry of Defence,” the statement said.

He also reported that Pakistani officials confirmed doing a “thorough search of government records” and could find no evidence of Pakistan’s ever giving consent to drone attacks.

But Pakistani officials clearly have countenanced the attacks in the past because they have benefited Pakistan’s own war against the Islamic radicals.

“I don’t care if they do it as long as they get the right people. We’ll protest in the National Assembly and then ignore it,” then-Prime Prime Minister Yousaf Raza Gilani was quoted as saying by then-U.S. ambassador Anne Patterson in 2008 in a leaked cable.

Karen DeYoung in Washington contributed to this story.