Britain's spies have been seeking guidance from an "ethical counsellor" on how to cope with moral dilemmas.
MI5 members have discussed issues like the rights and wrongs of extraordinary rendition and whether the Government was right to try to alter the ideological views of citizens.
The counsellor's existence was revealed yesterday in the Commons Intelligence and Security Committee's annual report. The post, created three years ago, is held by a former service director-general. Security reasons prevent the disclosure of his name. Senior figures dealing with the service's most sensitive work have been to see the senior adviser and some of the matters raised have led to wider debate within the organisation.
The report states that "concerns the individuals have raised include... whether there were sufficient controls for sharing information with countries that do not comply with international standards for the treatment of those in detention and whether guidance for staff on these matters was sufficiently accessible and understood."
Last week, the British Government admitted involvement in extraordinary rendition, where terror suspects were handed to the US in Iraq to be flown to Afghanistan for interrogation.
Lawyers for Binyam Mohammed, a British resident released from Guantanamo Bay, claim MI5 knew the US had used torture to obtain information from him, but the service denies this.
The issue of "whether it was ethical for the Government to seek to alter the ideological views of its citizens as part of its counter-radicalisation strategy" goes to the heart of government strategy that aims to use community campaigns to confront fundamentalism.
MI5 members questioned whether the service had adequate mechanisms to evaluate risks to the health of international counter-terrorism agents. The director-general of MI5, Jonathan Evans, has disclosed that 75 per cent of his agency's work is devoted to threats from Islamists, and that a large number of British Muslims, as well as local people in Pakistan and Afghanistan, are MI5 agents. The concern raised related to these field agents.
Logistics and seemingly a concern over resources also featured in discussions. Staff questioned whether MI5 should be involved in the Government's Prevent strategy, to prevent terrorism developing in communities, "given the pressure it faces to tackle the terrorist threat directly".
The report also said the service employed 3,382 people and expected that number to grow to 4,100 by 2011. Twelve of those employees have seen the counsellor so far.
The Commons Intelligence and Security Committee said: " It is reassuring that so few Security Service staff have felt the need to raise ethical concerns or complaints. We nonetheless welcome the establishment of the post and believe it provides an important avenue, should the need arise, for staff to discuss their concerns."
MI5 regrets that one employee did not access the counsellor, an officer whose partner was part of a secretly-filmed sadomasochistic session with Max Mosley. The officer revealed what happened to a newspaper. The officer was suspended and later resigned.
"The incident has highlighted the risks inherent in the vetting system," the report said. "The committee intends to look at this in more detail."