It has become almost a set piece of reports on newly fallen regimes: the discovery of confidential documents in abandoned or ruined offices that compromise those who previously held power. As some learnt to their cost in Iraq, such documents have to be treated with care; they may not be what they seem. The greater risk this time, with the documents found in an office that once belonged to Moussa Koussa, the head of Libya's security service, is that these documents are exactly what they seem: testimony to a relationship between Libya and Britain that, as the Prime Minister suggested to Parliament yesterday, "came too close".

There should, of course, be little surprise to the central allegation: that the US and British intelligence agencies co-operated with Muammar Gaddafi's security services and helped to track down his enemies abroad. And there is considerable irony in the fact that one of these appears to have been Abdelhakim Belhaj, who is now head of the Tripoli Military Council and one of the most powerful men in the new Libya. Not for the first time, yesterday's suspected terrorist is today's national leader. If all Mr Belhaj is asking for is an apology for what he says was his illegal "rendition" from Bangkok to a Tripoli prison in 2004, the US and British governments can probably count themselves very fortunate.

The truth is, however, that the fall of a regime has multiple repercussions. And the documents found in Tripoli raise a host of questions not just for the unsavoury Gaddafi regime, which is belatedly paying for its misuse of power, but for its one-time allies, chief among them Britain. David Cameron may have deftly switched sides when the scale of the Cairo protests suggested that the writing was on the wall for the region's long-time despots, but past relationships cannot be so easily expunged.

In fact, things could be a great deal worse for Mr Cameron and his ministers. They can, rightly, say they were not in power when the alleged renditions and torture of suspected terrorists took place, which also allows them to score party political points against Labour. They can also say – as Mr Cameron did yesterday – that they have acted to limit the damage, paying compensation to former Guantanamo prisoners and setting up the Detainee Inquiry, chaired by Sir Peter Gibson, to examine the Government's possible involvement in the improper treatment of detainees. The latest accusations, relating to eight or nine Libyans, fit into that framework, without the need for any new inquiry.

Yet it is not quite as simple as that. Governments and prime ministers may change, but the security services go on, and any damage to their international reputation inevitably reduces their effectiveness. It also reflects on the country and its political system as a whole. Claims about Britain's complicity with the US over rendition and torture – the knowledge of it, if not its actual use – cast a long shadow over our relations with many other, especially Muslim, countries. The present government knows this. Mr Cameron spoke yesterday of the need to "remove any stain on Britain's reputation" and "enable the security services to get on with the vital work they do".

It is essential, not just for British diplomacy, but for our standing and self-knowledge as a nation, to establish exactly how closely the government – and if not the government, then the agencies of state – collaborated with President Bush's post-9/11 "war on terror", and into what byways of iniquity they might have been led. Was the supposedly ethical foreign policy suborned by methods that were the very opposite?

These are matters for the Gibson inquiry. That such an inquiry should be necessary at all, however, demonstrates how inadequate existing oversight of the security services is. Yes, our national security needs to be guarded, but those guardians must themselves be accountable and trusted to be so. The documents turning up in Libya strongly suggest that they are not.