Foreign Secretary David Miliband and Home Secretary Alan Johnson, who are responsible for MI6 and MI5, said tough judgments had to be made in order to protect the UK from attack.
And they strongly denied allegations of a "policy to collude in, solicit, or directly participate in abuses of prisoners" or to cover up abuses.
Their defence, in a joint article for the Sunday Telegraph, came as another influential parliamentary committee raised serious concerns about the issue.
The Commons Foreign Affairs Committee said it was "imperative" that the Government fulfilled its legal obligations to act positively to prevent torture and to investigate allegations.
It expressed particular concern about Britain's relationship with Pakistan's Inter-Services Intelligence (ISI) agency, calling for an explicit assurance that UK officials would not be "uncritical of, or complicit in, abuses of human rights".
There have been a string of allegations about the involvement of UK intelligence agencies in the questioning of terrorist suspects abroad, including supplying questions for interrogators to ask.
Scotland Yard is conducting a criminal investigation into claims that MI5 was complicit in the abuse of Binyam Mohamed, a British resident who alleges that he was tortured while being held at sites in Pakistan, Morocco and Afghanistan.
Last week, the Parliamentary Joint Committee on Human Rights (JCHR) accused ministers of failing fully to answer questions on the issue and said an independent inquiry was the only way to restore public confidence in the intelligence and security agencies.
In the article, the ministers stressed that the UK "firmly opposes" torture and mistreatment but said there was not enough understanding of the tough judgments faced.
"There is no truth in suggestions that the security and intelligence services operate without control or oversight. There is no truth in the more serious suggestion that it is our policy to collude in, solicit, or directly participate in abuses of prisoners. Nor is it true that alleged wrongdoing is covered up," they wrote.
"These issues are of fundamental importance to our security and to our values. We need a public debate, but an informed one."
They said it was not possible to be certain about the behaviour of other governments "whose obligations may differ from our own".
"Yet intelligence from overseas is critical to our success in stopping terrorism. All the most serious plots and attacks in the UK in this decade have had significant links abroad.
"Whether passing information which might lead to suspects being detained, passing questions to be put to detainees, or directly interviewing them, our agencies are required to seek to minimise, and where possible avoid, the risk of mistreatment.
"Enormous effort goes into assessing the risks in each case. Operations have been halted where the risk of mistreatment was too high.
"But it is not possible to eradicate all risk. Judgments need to be made."
They also defended the Government's accountability on the issue, which was branded "woefully deficient" by the JCHR which called for the Intelligence and Security Committee (ISC), which is appointed by the Prime Minister to oversee the work of MI5 and MI6 and reports direct to Downing Street, to be reconstituted as a Parliamentary committee reporting to MPs.
The ministers said the ISC was an independent body that did not hesitate to criticise where necessary, adding: "The sensitive nature of the agencies' work requires a different set of checks and balances from other parts of government."
"We take all allegations of wrong-doing very seriously. The law is the ultimate safeguard and is available to those who feel their rights have been abused, as shown by current cases where individuals have brought claims against the Government," they added.
In its report, the FAC also accused the Foreign Office of "pulling its punches" over the "massive scale" of human rights abuses in Saudi Arabia, another key ally in the fight against terrorism.
It expressed concern that allegations continued to be made about the use of the giant American airbase on the British territory of Diego Garcia in the Indian Ocean for US "rendition" flights carrying terrorist suspects, urging ministers to press the US administration to carry out a comprehensive check of its records to establish whether there were any further cases beyond the two from 2002 which it admitted last year.
And it called on the Government to do more to address the concerns surrounding the treatment of detainees who had been captured by British forces in Iraq and Afghanistan and then handed on to the local authorities or the US.
Responding to the report, Amnesty International UK campaigns director Tim Hancock said: "This report is yet another voice in a growing chorus demanding greater transparency over the UK's involvement in 'war on terror' human rights abuses.
"It adds yet more weight to our call for a full, independent inquiry."
And James Welch, legal director of campaign group Liberty, said: "Calls for an independent judicial inquiry into the dirtiest part of Britain's 'war on terror' are becoming almost deafening.
"Is the Government listening? Will it appoint such an inquiry before it is eventually ordered by the courts?"
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