Prime Minister Tony Blair and President General Pervez Musharraf held two hours of talks, with both reinforcing their backing of a NATO-led mission to support the Afghan government, a Blair spokesman said.
The talks had threatened to be overshadowed by a military document obtained by the BBC that was critical of Pakistan's Directorate of Inter Services Intelligence, the country's top spy agency.
It reported that the document said "Pakistan is not currently stable but on the edge of chaos".
Mr Musharraf rejects the allegations that the ISI had indirectly supported terrorist groups and raised the issue with Mr Blair during their meeting.
"The president accepted that document is not government policy, so there was no further need to discuss it," said a spokesman for Blair's office.
He said Mr Blair also assured Mr Musharraf that British troops would remain in Afghanistan for the "long-term" as part of the NATO mission.
While Mr Musharraf told Mr Blair that he recognised the need to continue work to reduce cross-border activity between Pakistan and Afghanistan.
The meeting, at Blair's official country residence, Chequers, followed Mr Musharraf's visit to Washington, where he held discussions with US President George W Bush and Afghan leader Hamid Karzai.
Following that meeting it was decided that Afghanistan and Pakistan should have better intelligence coordination and interaction to meet the challenges of fighting militants.
But a news conference following a dinner revealed a frosty relationship between the leaders, with Mr Karzai and Mr Musharraf not shaking hands with each other, after shaking hands with Mr Bush.