Pakistan delivered a blunt message yesterday to America's new military commander for the region, warning General David Petraeus on his first international trip since taking the job that US missile strikes inside Pakistan must stop.

Petraeus, credited with pulling Iraq back from the brink, pointedly made Pakistan his first visit to the region, after last week assuming overall command of the Middle East and Central Asia, including Iraq and Afghanistan. Pakistan's co-operation is considered vital if the Taliban insurgency in Afghanistan is to be quelled, but Islamabad has been incensed by US missile attacks inside its territory against suspected militants.

"Continuing drone attacks on our territory, which result in loss of precious lives and property, are counterproductive and difficult to explain by a democratically-elected government. It is creating a credibility gap," Pakistan's president Asif Zardari told Petraeus, according to a statement issued by the president's office.

Petraeus also held meetings yesterday with Pakistani army chief Ashfaq Kayani and defence minister Ahmad Mukhtar, in which a similar message was reportedly conveyed. However, the strikes, which have intensified greatly over the past two months, killing dozens and causing uproar in Pakistan, are expected to go on.

Before 9/11 Pakistan had backed the Taliban government in Kabul, and its all-powerful army is believed to still support elements within the Taliban, seeing the Karzai government as allied with arch-enemy India.

"Pakistan has been targeting different Taliban factions than the US," said Farrukh Saleem, executive director of the Centre for Research and Security Studies, a thinktank based in Islamabad. "Pakistan is being encircled. There are Indian troops in the east, and Nato, the US and the Afghan national army to the west."

Analysts believe that the missile attacks are damaging an already weak civilian government in Islamabad, following the restoration of democracy earlier this year after more than eight years of military rule, providing an opening that anti-American Islamist politicians can exploit.

Last year Petraeus instigated a fresh approach in Iraq, with a "surge" of thousands of extra US troops and a successful ploy of separating the Sunni nationalist insurgents from al-Qaida, by turning the Iraqi Sunni Muslims against the global jihadists inspired by Osama bin Laden.

In Afghanistan the two key tenets of this counter-insurgency strategy are expected to be replicated.

"Petraeus does understand that, while the basic template from Iraq is applicable in Afghanistan and Pakistan, there are many differences," said Kamran Bokhari, director of Middle East analysis at Stratfor, a private US geopolitical intelligence firm. "The key difference is that Iraq was a sectarian conflict."

Petraeus used the threat of Shia Muslim dominance in Iraq to entice the Sunnis into the mainstream, whereas there are already large Sunni majorities in Afghanistan and Pakistan. Washington and Kabul are starting to engage in tentative talks with figures associated with the Afghan Taliban, but past attempts at winning over "moderate" Taliban have failed.

The US general will soon have a new boss following the US presidential election, with both candidates pledging to focus on Afghanistan and provide more troops, especially Barack Obama, who has repeatedly said that Afghanistan and Pakistan is where the fight against terrorism must be won.