Despite repeatedly denouncing the CIA’s drone campaign, top officials in Pakistan’s government have for years secretly endorsed the programme and routinely received classified briefings on strikes and casualty counts, according to top-secret CIA documents and Pakistani diplomatic memos obtained by The Washington Post.

The files describe dozens of drone attacks in the Tribal Areas and include maps as well as before-and-after aerial photos of targeted compounds over a four-year stretch from late 2007 to late 2011 in which the campaign intensified dramatically.

Markings on the documents indicate that many of them were prepared by the CIA’s Counterterrorism Centre specifically to be shared with Pakistan’s government. They tout the success of strikes that killed dozens of alleged al Qaeda operatives and assert repeatedly that no civilians were harmed.

Pakistan’s tacit approval of the drone programme has been one of the more poorly kept national security secrets in Washington and Islamabad. During the early years of the campaign, the CIA even used Pakistani airstrips for its Predator fleet.

But the files expose the explicit nature of a secret arrangement struck between the two countries at a time when neither was willing to publicly acknowledge the existence of the drone programme. The documents detailed at least 65 strikes in Pakistan and were described as “talking points” for CIA briefings, which occurred with such regularity that they became a matter of diplomatic routine. The documents are marked “top-secret” but cleared for release to Pakistan.

A spokesman for the Pakistani embassy in Washington did not respond to a request for comment. A CIA spokesman declined to discuss the documents but did not dispute their authenticity.

Prime Minister Nawaz Sharif reiterated his country’s objections to the drone campaign this week during his first visit to Washington since taking office this year.

CIA strikes “have deeply disturbed and agitated our people,” Nawaz said in a speech on Tuesday at the US Institute of Peace. “This issue has become a major irritant in our bilateral relationship as well. I will, therefore, stress the need for an end to drone attacks.”

He raised the issue in a meeting on Wednesday with President Barack Obama, “emphasising the need for an end to such strikes.” Nawaz did not publicly elaborate on how Pakistan would seek to halt a campaign that has tapered off but remains a core part of the Obama administration’s counterterrorism strategy.

The files serve as a detailed timeline of the CIA drone programme, tracing its evolution from a campaign aimed at a relatively short list of senior al Qaeda operatives into a broader aerial assault against militant groups with no connection to the September 11, 2001, attacks.

The records also expose the distrust and dysfunction that has afflicted US-Pakistani relations even amid the undeclared collaboration on drone strikes.

Some files describe tense meetings in which senior US officials, including then-secretary of state Hillary Clinton, confront their Pakistani counterparts with US intelligence purporting to show Pakistan’s ties to militant groups involved in attacks on American forces, a charge that Islamabad has consistently denied.

In one case, Clinton cited “cell phones and written material from dead bodies that point all fingers” at a militant group based in Pakistan, according to a Pakistani diplomatic cable dated September 20, 2011. “The US had intelligence proving ISI was involved with these groups,” she is cited as saying, referring to Pakistan’s Inter-Services Intelligence agency.

In a measure of the antagonism between the two sides, a 2010 memo sent by the Ministry of Foreign Affairs to its embassy in Washington outlined a plan to undermine the CIA.

“Kindly find enclosed a list of 36 US citizens who are [believed] to be CIA special agents and would be visiting Pakistan for some special task,” said the memo, signed by an official listed as the country’s director general for Americas. “Kindly do not repeat not issue visas to the same.”

The earliest of the files describes 15 strikes from December 2007 through September 2008. All but two of the entries identify specific al Qaeda figures as targets.

The campaign has since killed as many as 3,000 people, including thousands of militants and hundreds of civilians, according to independent estimates.

There have been 23 strikes in Pakistan this year, far below the peak in 2010, when 117 attacks were recorded. The latest strike occurred September 29, when three alleged fighters with ties to the militant Haqqani network were killed in North Waziristan, according to news media reports.

Several documents refer to a direct Pakistani role in the selection of targets. A 2010 entry, for example, describes hitting a location “at the request of your government”. Another from that year refers to a “network of locations associated with a joint CIA-ISI targeting effort”.

The files also contain fragments of code words — including SYL-MAG, an abbreviation of Sylvan Magnolia — that correspond to covert drone operations. The code word was later changed to Arbor-Hawthorn.

In time, the CIA identified so many suspected al Qaeda and militant compounds that it gave them coded designations, including MSC 215 for a Miran Shah Compound where explosives were manufactured and SC 5 for Spailpan Compound number 5 in South Waziristan.

The dates and number of strikes generally correspond with public databases assembled by independent groups, indicating that those organisations have reliably tracked drone attacks from media reports, even if the number of civilian casualties has often been a source of dispute.

The documents confirm the deaths of dozens of alleged al Qaeda operatives, including Rashid Rauf, a British citizen killed in 2008 who “helped coordinate al-Qaeda’s summer 2007 plot to blow up transatlantic flights originating from Great Britain”, one memo said.

But the documents also reveal a major shift in the CIA’s strategy in Pakistan as it broadened the campaign beyond “high-value” al Qaeda targets and began firing missiles at gatherings of low-level fighters.

The files trace the CIA’s embrace of a controversial practice that came to be known as “signature strikes”, approving targets based on patterns of suspicious behaviour detected from drone surveillance cameras and ordering strikes even when the identities of those to be killed weren’t known.

At times, the evidence seemed circumstantial.

On January 14, 2010, a gathering of 17 people at a suspected Taliban training camp was struck after the men were observed conducting “assassination training, sparring, push-ups and running”. The compound was linked “by vehicle” to an al Qaeda facility hit three years earlier.

On March 23, 2010, the CIA launched missiles at a “person of interest” in a suspected al Qaeda compound. The man caught the agency’s attention after he had “held two in-car meetings, and swapped vehicles three times along the way”.

Other accounts describe militants targeted because of the extent of “deference” they were shown when arriving at a suspect site. A May 11, 2010, entry noted the likely deaths of 12 men who were “probably” involved in cross-border attacks against the US military in Afghanistan.

Although often uncertain about the identities of its targets, the CIA expresses remarkable confidence in its accuracy, repeatedly ruling out the possibility that any civilians were killed.

One table estimates that as many as 152 “combatants” were killed and 26 were injured during the first six months of 2011. Lengthy columns with spaces to record civilian deaths or injuries contain nothing but zeroes.

Those assertions are at odds with research done by human rights organisations, including Amnesty International, which released a report this week based on investigations of nine drone strikes in Pakistan between May 2012 and July 2013. After interviewing survivors and assembling other evidence, the group concluded that at least 30 civilians had been killed in the attacks.

White House spokesman Jay Carney acknowledged Tuesday that drone strikes “have resulted in civilian casualties” but defended the program as highly precise and said there is a “wide gap” between US estimates and those of independent groups.

Several of the files are labelled as “talking points” prepared for the DDCIA, which stands for deputy director of the CIA. Michael J Morell, who held that position before retiring this year, delivered regular briefings on the drone program to Husain Haqqani, who was the Pakistani ambassador to the United States at the time.

The CIA also shared maps and photographs of drone operations in Pakistan that have not previously been shown publicly. The maps contain simplistic illustrations, including orange flame emblems to mark locations of strikes. The photos show before-and-after scenes of walled compounds and vehicles destroyed by Hellfire missiles, some marked with arrows to identify bodies amid the rubble.

The documents indicate that these and other materials were routinely relayed “by bag” to senior officials in Islamabad.

When contacted Wednesday, Haqqani declined to comment and said he would not discuss classified materials.

In one case, Morell indicated that the CIA was prepared to share credit with the Pakistanis if the agency could confirm that it had killed Ilyas Kashmiri, an al Qaeda operative suspected of ties to plots against India. The agency would do so “so that the negative views about Pakistan in the US decision and opinion making circles are mitigated,” according to a diplomatic memo.

But Morell was also sent on occasion to confront Pakistan with what US officials regarded as evidence of the nation’s support for terrorist groups. In June 2011, he arrived at the embassy with videos showing militants scrambling to clear materials from explosives plants that the United States had discovered and called to the attention of counterparts in Pakistan.

Rather than launching raids, the Pakistanis were suspected of tipping off the militants, who dispersed their materials in a “pickup truck, two station wagons and at least two motorcycles to multiple locations in South Waziristan”, according to the memo summarizing the meeting with Morell.