Bitter disputes over covert CIA activities and drone attacks inside Pakistan, lack of progress over peace talks in Afghanistan, and rising Islamist-led opposition to the presence of foreign forces in the region are fuelling the biggest crisis in US-Pakistan relations since the 9/11 attacks, Pakistani politicians, army sources and intelligence officers say.

An activist of the Jamaat-i-Islami party holds a burning effigy of Raymond Davis during a protest in Peshawar. A senior security official official warned that the new US military offensive in Afghanistan masterminded by General David Petraeus, and the accompanying rise in casualties, were making it more difficult to achieve a peace settlement. "The whole idea that a big military surge would induce the other side to ask for reconciliation is flawed. It goes against the whole history of Afghanistan."(Photo: AFP/GETTY) Pakistan is seen by Washington and London as a vital ally in the "war on terror", while the Pakistani government and army say they remain committed partners 10 years after the Afghan conflict began.

But harsh US criticism of Islamabad's counter-terrorism campaigns in Pakistan's western tribal areas, repeated in a White House report last week, and "blowback" from the US military surge in Afghanistan are testing the relationship to breaking point, officials warn.

"We will not accept the stigmatising of Pakistan," said Salman Bashir, Pakistan's foreign secretary. "We need to re-examine the fundamentals of our relationship with the United States to get greater clarity. There has been a pause. Now we must start again."

Rehman Malik, Pakistan's interior minister, said the Americans should stop blaming others for their difficulties in Afghanistan, where violence has worsened in the past year and reconciliation efforts have made little progress. "If the strategy is not right, all the stakeholders have to share responsibility," Malik said.

Pakistan had suffered "unimaginably" since the "war on terror" began, he added. "We are not just fighting for Pakistan, we are fighting for the whole world. If this country is destabilised, the whole region is destabilised … so please, stop the blame game. We are your partners. We are victims, not part of the terrorists."

The rift comes at a dangerous moment for the US and its Nato allies as the Afghan conflict enters the "endgame" and they begin the process of handing over control of security to Afghan forces – and start withdrawing troops in July.

US criticism of Pakistan centres on ongoing suspicions that its powerful spy agency, the Inter-Services Intelligence Directorate (ISI), continues to support Taliban and other militant groups active in Afghanistan and Kashmir, partly in a bid to retain influence over a post-withdrawal government in Kabul. Last week members of a US congressional committee accused Pakistan of playing a double game, while the White House described its counter-terrorism efforts in tribal areas as disappointing.

Pakistani anger focuses in turn on three main areas: unauthorised CIA activity inside the country, Pakistan's perception that the US is keeping it "out of the loop" on Afghanistan, particularly in respect of mooted peace talks with the Taliban, and what Islamabad sees as the US failure to appreciate the full cost and impact of the "war on terror" on Pakistan's economy and social cohesion.

"The main problem we face is the presence of foreign forces in Afghanistan. This is the main problem for the whole region," an intelligence official said. "The 'war on terror' fuels extremism in Pakistan's society."

Unmanned drone missile attacks launched by the CIA at targets inside the tribal areas bordering Afghanistan have inflamed anti-US feeling in Pakistan, making it increasingly difficult to justify the continuing "war on terror" alliance, a senior security official said.

"In the long term, it [the drone attacks] is completely counter-productive because it alienates the population and restricts our ability to shape our security environment," the official said.

Pakistan's army had conducted several campaigns to suppress Taliban groups and al-Qaida operatives and sympathisers in Pakistan since 2001, including in South Waziristan and Bajaur as well as in Swat, north of Islamabad, the official said. But the army was resisting US pressure to launch another offensive in north Waziristan. "What do they [the US] want us to do? Declare war on our whole country?" the official asked.

"The Americans need to devise a strategy but better still, share the [drone] technology with us," interior minister Rehman Malik said. "There is big anti-American feeling. We would like to urge that the drone attacks be stopped."

Tensions over CIA activities peaked earlier this year when Pakistan arrested a CIA contractor, Raymond Davis, after a shooting incident. Davis was publicly named, held in detention for 47 days and interrogated, before eventually being released after payment of $2.3m in compensation. The affair followed the withdrawal last December of the CIA station chief in Pakistan after his name was published in local media – an unprecedented security breach.

Whether by coincidence or design, a drone attack last month, launched the day after Davis was released, killed dozens of people in north Waziristan and sparked widespread outrage. The Pakistani army chief, General Ashfak Kayani, called the attack a "violation of human rights" and said the dead were tribal leaders, not terrorists. The prime minister, Yousaf Raza Gilani, called the attack "irrational".

Pakistan has since moved to expel hundreds of US personnel, many of whom are believed to work for the CIA or US special operations, by not renewing their visas.

In a tacit acknowledgement of how serious the rift has become, the US invited General Ahmed Shuja Pasha, head of the ISI, for talks in Washington this week. Pasha is understood to have met Leon Panetta, the CIA director, and Admiral Mike Mullen, chairman of the US joint chiefs of staff. There have been no further drone attacks since the Waziristan strike.

Salman Bashir, Pakistan's foreign secretary, said Pakistan was deeply concerned about the apparent lack of progress in reconciliation efforts in Afghanistan. Bashir said Pakistan welcomed some of the steps taken so far, such as the establishment of the Afghan High Peace Council and attempts to reintegrate Taliban foot soldiers.

But he said the peace process could not be left to the Afghan government alone. He questioned how serious the US was about direct talks with the Taliban leadership – and whether such a process was even feasible – while complaining that Pakistan was being kept in the dark about US intentions.

"It's between the Americans and the [Afghan] opposition. But we don't know who the opposition is. To start with it was al-Qaida and the Taliban. Now it's al-Qaida affiliates and other groups. So who do you talk to? Is it Mullah Omar? Are there preconditions or end conditions? We need to sort this out," Bashir said.

There was a lack of "strategic coherence" about the US approach in Afghanistan and a growing sense of urgency as the July deadline for the beginning of US troop withdrawals neared, he added.

Bashir is expected to hold fence-mending talks in Washington later this month. Depending on the outcome, Pakistan's president, Asif Ali Zardari, may make his first official visit to Washington in May.

The senior security official said Pakistan could only help the Americans in Afghanistan if it knew what their strategy was. "Share it with us. What is your plan? Do you plan to stay for five years, for 20?"

But the official warned that the new US military offensive in Afghanistan masterminded by General David Petraeus, and the accompanying rise in casualties, were making it more difficult to achieve a peace settlement.

"The whole idea that a big military surge would induce the other side to ask for reconciliation is flawed. It goes against the whole history of Afghanistan."