Tony Blair has assured the president of Pakistan that a leaked paper condemning the country's intelligence service does not reflect his government's view.
Blair and Musharraf met at Chequers
A researcher at the Ministry of Defence claimed that Pakistan's intelligence service, ISI, had indirectly helped the Taleban and al-Qaeda.
But after two hours of talks, Downing Street said President Pervez Musharraf had accepted Mr Blair's reassurances.
And the president said he was resolute in dealing with the extremists.
He told Mr Blair he was determined to deal with the Taleban and reduce the level of activity across the border into Afghanistan, said the spokesman for Number 10.
The prime minister thanked Gen Musharraf for Pakistan's help in the so-called war on terror.
And the president expressed his thanks for the help supplied by the UK in the aftermath of last year's earthquake in Pakistan.
The document, leaked to the BBC, said Pakistan's intelligence service, the ISI, should be dismantled.
It also said the UK went into Afghanistan "with its eyes closed", and revealed that a secret deal to extricate UK troops from Iraq so they could focus on Afghanistan failed when British military leaders were overruled.
And it said the Iraq war had "acted as a recruiting sergeant for extremists across the Muslim world".
But an MoD spokesman said "the academic research notes quoted in no way represent the views of either the MoD or the government".
British defence officials have said the paper was written by a junior official, that it was unfinished and had not been seen by anyone who actually makes government policy.
And senior intelligence sources told BBC defence and security correspondent Rob Watson that, while the relationship with the ISI is not perfect, co-operation has improved beyond all recognition since 9/11 and the attacks in London last year.
Labour MP Khalid Mahmood said radical Islamic groups existed all over the world, including in the UK, where extremists last year killed 52 people in suicide bomb attacks on 7 July.
"I don't think they just exist in Pakistan, I think if you look at the people that have been going on in 7/7, radicalised in the UK, this is not one organisation that is based in just one part of the world.
"Whether you go to Indonesia, whether you go to Europe, whether you go to the US, you'll find pockets of these people that have set up."
"I think what we've got to do is to tackle that head on, rather than finger pointing at one individual country or one individual place."
Gen Musharraf, who met Tony Blair at Chequers, told the BBC's Newsnight he was "fully satisfied" with Pakistan's co-operation in the fight against terrorism.
"There is perfect co-ordination going on - intelligence and operational co-ordination at the strategic level, at the tactical level," he said.