Asif Ali Zardari, Pakistan’s president, has rejected the Obama administration’s strategy of linking policy on Pakistan and Afghanistan in an effort to end a Taliban insurgency and bring stability to the region.

“Afghanistan and Pakistan are distinctly different countries and cannot be lumped together for any reason,” Mr Zardari said in an interview with the Financial Times on the anniversary of his first year in office.

Barack Obama, US president, appointed Richard Holbrooke , a senior diplomat who helped end the Bosnian war, as his special representative to Pakistan and Afghanistan this year in a move intended to address the two states as a single arena of conflict.

Mr Zardari’s comments reflect Pakistan’s unwillingness to be aligned in a joint policy framework with neighbouring Afghanistan, an approach referred to as “AfPak”.

The Pakistani leader and his senior officials draw a distinction between a Pakistan with functioning institutions, diversified economy and a powerful national army, and Afghanistan, a state shattered by decades of conflict and ethnic divisions.

Ending the Taliban insurgency raging on both sides of the border between Afghanistan and Pakistan is only likely to be achieved by concerted military action by Nato forces fighting in Helmand and Kandahar and Pakistan’s army in Waziristan and other tribal areas along the border. Military experts said Taliban leaders travel across the Durand Line, the colonial era border, to avoid military pursuit.

Mr Holbrooke’s two-country mandate was also a recognition of Pakistan’s historic role in supporting the Taliban regime ousted from Kabul in 2001, and Islamabad’s former doctrine of “strategic depth” into Afghanistan in case of a conflict with arch-rival India.

The US state department on Thursday spoke out in defence of its approach. “The US treats Afghanistan and Pakistan as two countries, but facing a common challenge presented by violent extremism,” said Ian Kelly, state department spokesman. “Our efforts centre on the president’s goal to dismantle, disrupt, and defeat the extremist threat faced in both countries.”

Mr Zardari said Mr Holbrooke had brought a “unique focus on relations with Pakistan” and acknowledged the emphasis that Mr Obama had put on Pakistan’s economic and energy needs.

The appeal by the husband of slain former prime minister Benazir Bhutto for individual, rather than joint, focus came before a high profile meeting with Mr Obama and Gordon Brown, the UK’s prime minister, in New York this month and a visit next month to Islamabad by Hillary Clinton, the US secretary of state.

At these meetings, Mr Zardari is expected to appeal for more financial assistance to his country, which he says is essential to ending the menace of terrorism.

“Pakistan does not have the luxury of time. Given the severity of internal security challenge the country is facing, it is critical that the economy is provided a strong stimulus as quickly as possible so that the maximum number of jobs are created in the shortest time,” he said.

“If [international aid flows] are delayed beyond the next few months, the country will be forced to cut development spending as well as the provision of critical social services. You can then imagine how big a setback that could be for the global war on terror.”

The UN warned on Thursday that many Pakistanis who had returned home after fleeing fighting between the army and the Taliban in the north-west of the country said they cannot survive for more than two weeks without aid.

The UN estimated that more than two-thirds of the 2.7m displaced by the conflict had gone home.

Many analysts say Pakistan and Afghanistan have a shared history and were badly affected by geopolitical shifts in the 20th Century.

“You have to remember we are young countries trying to find our feet," Talat Masood, a retired general and security analyst, said. “We are on the fault lines of the end of three empires: the Ottoman Empire, the British and the Soviet. September 11 and the War on Terror came at the end of all that.”

Many Pakistani officials regard the AfPak formulation as “insulting”, and resist comparison between what they see as their own modern state and the fractious peoples of Afghanistan.

Diplomats while acknowledging that the terminology is unpopular say it does reflect an operational reality in fighting al-Qaeda and Taliban militants. “One of the realities of talking about AfPak is that you can’t crack these problems without putting pressure on both sides,” said one.

The New York summit between Mr Obama, Mr Zardari and Mr Brown this month is seen as an opportunity to give Pakistan individual focus and undo some of the slight caused by the AfPak approach. The summit by the Friends of Democratic Pakistan grouping aims to push forward Pakistan’s recovery strategy and deepen aid commitments.