The new generation of secret courts proposed by the government could suppress evidence of British collusion in torture, according to the chief UN official responsible for investigating wrongdoing by security and intelligence agencies.

Concern about the government's plan – contained in the justice and security bill – was expressed by Prof Juan Méndez, the UN's special rapporteur on torture. "If a country is in possession of information about human rights abuses, but isn't in a position to mention them, it hampers the ability to deal effectively with torture," he said. Méndez, himself a victim of torture in his native Argentina in the 1970s, was speaking at the thinktank Chatham House on Monday night.

After attacking the US for what he called the "extensive use of state secrets" to suppress evidence of torture and other abuses, Méndez referred to the so-called control principle, which allows governments to determine how its intelligence can be used once shared with another state.

Ministers maintain that the new secret courts are needed to protect its intelligence-sharing relationship with the US and other governments, while critics say they are intended to conceal evidence of crimes committed by the British government, including involvement in the rendition and torture of British citizens suspected of being terrorists.

The issue was at the centre of high court hearings about the treatment of Binyam Mohamed, the Ethiopian-born UK resident secretly rendered to Guantánamo Bay after being seized in Pakistan in 2002.

The high court ruled that CIA information that revealed MI5 and MI6 knew of Mohamed's ill-treatment should be disclosed. The ruling provoked a storm of protest, with some in the government claiming the US had threatened to withhold intelligence from the UK.

At the same time, to avoid further incriminating evidence being disclosed, the UK government paid undisclosed sums, believed to amount to millions of pounds, in an out-of-court settlement to British citizens and residents who had been incarcerated in Guantánamo Bay.

The government responded by introducing the justice and security bill, which would prevent the disclosure of any information in the hands of the security and intelligence agencies from being disclosed in civil cases.

Méndez said the control principle might be a good way of maintaining a good working relationship with other governments but could hinder attempts to suppress torture.

He said he had expressed his concerns to the British government during discussions over the decision to suspend the work of the Gibson inquiry, the commission appointed by David Cameron in 2010, after police announced they were investigating the UK's role in the rendition of Libyan dissidents and their families to Tripoli in 2004.

While describing the talks as "confidential", Méndez said he had specifically raised the problems that could be caused by the control principle and what he called the "important issue" of governments "aiding and abetting torture" by agents of other countries.

In a clear reference to the treatment of terror suspects after the 11 September 2001 attacks on the US, Méndez said torture had been used by states that claimed to be the strongest supporters of human rights.

Defending the government's proposals, a Cabinet Office spokesperson said: "Under the government's plans, nothing currently heard in open court could be heard in secret. Civil cases which are currently not heard at all – including cases where mistreatment is alleged – will be able to be fully investigated and scrutinised by the courts. The government has been clear that it stands firmly against torture and cruel, inhuman and degrading treatment or punishment."

In the European parliament, the Liberal Democrat European justice and human rights spokeswoman, Sarah Ludford, criticised EU states for failing to meet their obligations to carry out full, independent inquiries to investigate human rights violations.

Referring to a report into alleged transportation and illegal detention of prisoners in European countries by the CIA, she said: "It's vital that member states support independent inquiries to ascertain and secure accountability for their complicity in rendition and torture, without which we risk eroding citizens' trust in the democratic institutions of the EU to protect and promote our human rights."