But Foreign Secretary David Miliband and Home Secretary Alan Johnson said it was impossible to remove all risk when using intelligence obtained overseas.
This came as a committee of MPs urged a probe into the transfer of terror suspects through UK territories.
Last week a committee of MPs and peers called for an independent inquiry into claims of UK complicity in torture.
The Joint Human Rights Committee said on Tuesday the government had not done enough to investigate these claims, because it had been unable to establish whether British officers were involved in mistreatment.
Now the Foreign Affairs Select Committee has also said it has grave concerns that British officers were complicit in torture.
But in a joint article in the Sunday Telegraph Mr Miliband and Mr Johnson said the UK "firmly opposed" torture and cruel, inhuman and degrading treatment or punishment.
They said there was "no truth" in suggestions it was official policy to "collude in, solicit, or directly participate in abuses of prisoners".
But "difficult judgments and hard choices" had to be made, they added, and while anyone detained in the UK would be treated well, the same guarantee could not be made about those held by foreign authorities.
"Operations have been halted where the risk of mistreatment was too high. But it is not possible to eradicate all risk," they wrote.
The pair, whose departments are responsible for Britain's intelligence services, were responding to Tuesday's report, but MPs on the Foreign Affairs Select Committee also want action to ensure Britain is not complicit in torture.
Its chairman Labour MP Mike Gapes said: "The government has a duty to use information that comes into its possession, from whatever source and however obtained, if it believes this will avert the loss of life.
"At the same time, we strongly recommend that the government should continue to exert as much persuasion and pressure as possible to try to ensure world-wide that torture is not employed as a method of interrogation."
The committee also said there had been inadequate investigation into the transportation of two men through the American airbase on the small British Indian Ocean territory of Diego Garcia.
It said the government had a "moral and legal obligation" to ensure UK airspace and airports were not for rendition - which is the transfer of suspects to countries where torture is carried out.
And it urged ministers to pile pressure on the US to carry out a comprehensive check of its records to establish whether there have been other cases beyond two from 2002 it admitted last year.
The report warned of the dangers of turning a blind eye while using information obtained in countries known for their human rights abuses.
It said: "There is a risk that use of evidence which may have been obtained under torture on a regular basis... could be construed as complicity in such behaviour."
The committee had particular worries over Britain's relationship with Pakistan's Inter-Services Intelligence (ISI) agency, whose practices give "cause for great concern".
It also accused the Foreign Office of "pulling its punches" over the "massive scale" of human rights abuses in Saudi Arabia.
Mr Gapes also called on the government to publish the previous guidelines given to intelligence officers on the questioning of detainees overseas.
Scotland Yard is conducting a criminal investigation into claims MI5 was complicit in the abuse of Binyam Mohamed, a British resident who says he was tortured while being held at sites in Pakistan, Morocco and Afghanistan.
Amnesty International UK campaigns director Tim Hancock described the Foreign Affairs Select Committee report as "yet another voice in a growing chorus demanding greater transparency over the UK's involvement in 'war on terror' human rights abuses".
He also demanded a full, independent inquiry.
"The committee rightly asks some very pointed questions about the use of UK airspace and territory, particularly Diego Garcia, in US rendition operations," he said.
"Britain should stand firm in its opposition to torture, both through our words and our actions."
Andrew Tyrie, the Tory MP who chairs the All Party Parliamentary Group on Extraordinary Rendition, said an inquiry should be held immediately.
"Neither the investigation by the police into the Binyam Mohamed case nor the other civil actions brought should stand in the way of getting to the bottom of this," he said.
"It is the only way to give the public confidence that we have got to the bottom of all of this, to draw a line under it and to move on."