US secretary of state Condoleezza Rice has issued a stern warning to Pakistan over Islamabad’s strategy of offering a truce to militants operating along the lawless Afghan border.

Rice said on Wednesday that Washington had made it “very clear” that any deal with terrorists will come back “first and foremost” to “haunt Pakistan.”

Since 2001, Pakistan has been a front-line state in the US-led war on terror and a recipient of billions of dollars of US aid intended to fund the fight against the Taliban and Al-Qaida.

Rice said that Washington is “concerned that any deal with the region would be very clear that terrorists cannot be harboured, terrorists cannot operate with impunity, because ultimately that’s going to come back, first and foremost, to haunt Pakistan. It will haunt the rest of us too, but first and foremost, it’s going to haunt Pakistan.”

The secretary of state was asked whether US military objectives in Afghanistan were compatible with the new Pakistani government’s policy of engaging militants.

Democratic presidential candidate Senator Barack Obama earlier this week said he had “repeatedly challenged George Bush and John McCain’s refusal to hold the Pakistani government accountable for inability to crack down on Al-Qaida and Taliban operating within their borders.”

“We are not going to get Afghanistan right until we get our Pakistan policy right," Obama had said.

Rice acknowledged that “it is obviously the sovereign state of Pakistan’s right to handle this situation,” but in the same breath added that President George W. Bush’s administration had “made it very clear to the Pakistani government that the extremists who operate in the Northwest frontier in the Federal Administered Tribal Areas are a threat to them and to us and to everybody on the globe, and that we have a common goal and a common objective in making sure that they cannot operate.”

She pointed out that the “forces of some of those people, some of those extremists,” assassinated former Pakistani Prime Minister Benazir Bhutto. “So we have a common objective here,” she added.

She noted that the provinces along the border have not been governed for “years and years and years” and said the US was trying to develop with the new Pakistani government a “positive agenda for that region.”

But she said for this agenda to work “you have to be willing to make sure that the bad forces are destroyed and you have to be willing to give the population another chance.”

She acknowledged the new government was facing a difficult time as it tries to settle in, but said, “We’re prepared to help, and we’re prepared to help with a better life for the population, and we’re prepared to help in helping them to get the means to deal with this area where terrorists who are a threat to them as well as us, are lodged.”

Earlier this month, a prominent US think tank accused individuals within the Pakistani government of supporting the Taliban and other terrorist groups operating along the Afghanistan-Pakistan border.

The RAND Corporation study concluded that if Taliban “sanctuary bases” in Pakistan are not eliminated, the United States and its NATO allies will face “crippling long-term consequences” in their effort to stabilise and rebuild Afghanistan. The Pakistani government promptly dismissed the report as baseless.

The study, funded by the US Department of Defence, found that Pakistan's Inter-Services Intelligence Directorate and Frontier Corps have failed to eliminate Afghan insurgent groups based in Pakistan.

It also accused individuals from these Pakistani organisations of having provided direct assistance to groups like the Taliban and Haqqani network.

Report author Seth Jones, a senior political scientist at RAND, said, "Right now, the Taliban and other groups are getting help from individuals within Pakistan's government, and until that ends, the region's long-term security is in jeopardy."

Jones said, “Solving this problem will require a difficult diplomatic feat: convincing Pakistan's government to undermine the sanctuary on its soil.”