Pakistan has been accused of detaining hundreds of alleged terror suspects without legal process by human rights organisation Amnesty International.
Some of the detainees ended up in Guantanamo Bay
The group says some were tortured or otherwise ill-treated, others were sold to the US military, and others have vanished without trace.
Pakistan denies torture, but detentions without legal process are taking place, a government spokesman told the BBC.
The report comes while the Pakistani leader is visiting the UK.
Some of the missing, says Amnesty, were known al-Qaeda suspects, but others included women and children.
A government spokesman told the BBC that the attacks of 11 September 2001 had required new measures to be taken.
He denied the allegations of torture and enforced disappearances.
President Pervez Musharraf had earlier denounced a British Ministry of Defence (MoD) research paper that accused Pakistani security forces of indirectly helping al-Qaeda and the Afghan Taleban.
After two hours of talks with Prime Minister Tony Blair on Thursday, a UK government spokesman said Gen Musharraf had accepted assurances that the document did not represent government policy.
The accusations in Amnesty's report are based in part on testimony from former detainees at the US military prison at Guantanamo Bay, Cuba, who have since been released without charge.
Evidence from the families of those who have disappeared was also used.
The report says the clandestine nature of the detentions means it is impossible to know how many are still being held in secret locations.
The rights group called on Gen Musharraf to set up a central list of detainees to end the practice of illegal abduction.
"Enforced disappearances were almost unheard of in Pakistan before the start of the US-led war on terror. Now they are a growing phenomenon, spreading beyond terror suspects," Amnesty researcher Angelika Pathak said.
In the MoD research paper denounced by the Pakistani leader, a researcher said Pakistan's intelligence service, ISI, had indirectly helped the Taleban and al-Qaeda.
The document, leaked to the BBC, said 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".
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.
Gen Musharraf, who met Tony Blair at his country residence, 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.