Cynics might suggest that there was no way that a member of the British security services was ever going to be brought to trial over allegations that the UK colluded in the mistreatment of terrorism suspects in Afghanistan, Pakistan and Libya. But there is more to it than simply a security establishment anxious to avoid lengthy and embarrassing court proceedings prying into institutions which prefer to operate in secrecy.

British officials were never accused directly of torture, but rather of turning a blind eye to the practices of the US and its Arab allies, and also of providing the intelligence upon which some maltreated individuals were quizzed. With such vague and unprovable connections, it was never likely there would be enough evidence to prosecute individual British agents. And so a three-year police investigation concluded yesterday. The outcome does not exonerate the British security services, but neither should all the charges made by terrorism suspects be accepted at face value.

More important even than the individual cases – appalling though they may be – is the unresolved suspicion that, despite an official position which repudiates torture, the secret services have been authorised to pursue dubious, complicit practices by those at the highest levels. That the orders might even have come from government ministers only adds to the pressure for answers.

There is an inquiry into the treatment of detainees that is due to begin under the chairmanship of a retired judge, Sir Peter Gibson, as soon as any potential court cases are held or dismissed. But several human rights groups – including Liberty and Amnesty International – are to boycott the proceedings, both because there will be no evidence from any alleged victims and because the Government will decide which parts of the inquiry should be held in secret. To restore the credibility of this all-important inquiry, the Prime Minister should look again at its terms of reference and make it more open.

Meanwhile, yesterday's decision from the police and Crown Prosecution Service to investigate allegations of the "rendition" of Libyan asylum-seekers back to Tripoli is to be applauded. There is certainly evidence that needs explanation. One of the dissidents handed over to Colonel Gaddafi's torturers was Abdel Hakim Belhaj, who later became one of the leaders of the independence movement which seized power in Libya last year. And when Gaddafi fell, documents discovered in Tripoli suggested his rendition may have been authorised by Sir Mark Allen, then MI6's head of counter-terrorism. That both Sir Mark and his boss, the then Foreign Secretary Jack Straw, will be questioned by police, is only right.

That said, with the intelligence and political communities both gearing up to point the finger at each other, the Libyan rendition investigations may also struggle to reach a final conclusion. Equally, it may founder on legal distinctions between "extraordinary rendition" and "judicial rendition". Even more reason for the Gibson inquiry to be beefed up.

It is difficult to overstate the scale of what is at stake. As the Foreign Secretary has rightly observed, the allegations by themselves gravely undermine Britain's reputation as a country that upholds international law. The Deputy Prime Minister was yesterday insistent that the Government "completely condemns torture and inhumane treatment". But what is needed now is more than words. Disturbing questions have been raised about where Britain draws the line between decency and realpolitik. There may not be the evidence to prosecute British individuals, but Britain itself still stands accused. Between them, the courts and the Gibson inquiry must uncover the truth.