A controversial court that claims to be completely independent of the British government is secretly operating from a base within the Home Office, the Guardian has learned.

The Investigatory Powers Tribunal, which investigates complaints about the country's intelligence agencies, is also funded by the Home Office, and its staff includes at least one person believed to be a Home Office official previously engaged in intelligence-related work.

The discovery that the IPT is lodged within a Whitehall department comes at a time when the Nick Clegg, the deputy prime minister, is commissioning a review into the intrusive capabilities of UK intelligence agencies and the legal framework in which they operate.

In a speech to the the intelligence and military thinktank the Royal United Services Institute this week, he argued that greater transparency was needed at the IPT.

Labour's leader, Ed Miliband, has also argued that the system for oversight of the UK's intelligence agencies is in need of reform, and the shadow home secretary, Yvette Cooper, said a debate about oversight was long overdue.

The disclosure that the IPT operates inside the Home Office is likely to fuel criticisms of the court that have been levelled by rights groups, lawyers and complainants.

The tribunal was created in October 2000 by the Regulation of Investigatory Powers Act and given the power to investigate any complaints against GCHQ, MI5 or MI6, as well as complaints about surveillance operations mounted by the police or any other public bodies.

Since then it has investigated about 1,500 complaints, and upheld 10 – although five of these concerned members of one family who had all lodged complaints about surveillance by their local council.

The president of the IPT, Sir Michael Burton, a high court judge, has said this low figure is explained in part by the large number of "frivolous, vexatious" complaints that it receives, and because some complainants are paranoid, saying in a speech last year that the tribunal attracted people who insisted that MI5 had planted listening devices in their teeth.

Burton also argues that the tribunal needs to conduct much of its work behind closed doors in order to secure the trust and complete co-operation of the agencies whose conduct it investigates.

In a BBC radio interview last year he said the agencies had a statutory obligation to disclose anything of relevance to a complaint. "There is nothing we cannot see," he said. "We are confident that we are shown everything."

However, the IPT will not say whether GCHQ had disclosed the existence of its bulk surveillance operations, which attempt to capture the digital communications of everybody – including those people who complain to the tribunal.

Nor will it disclose whether it has issued any secret ruling on the lawfulness of those operations, on the grounds that the rules under which it operates stipulate that it cannot do so without the permission of GCHQ itself. It has not sought that permission on grounds it knows it would not be given.

The IPT's critics complain that the secrecy is excessive and that its procedures are stacked so heavily in favour of the government and against complainants that it is fundamentally unfair. Some senior lawyers describe the IPT as "Kafkaesque", while one eminent barrister dismisses it as "a kangaroo court".

The tribunal's critics have included Lord Dyson who, as Master of the Rolls, is the second most senior judge in England and Wales. Last year, when Scotland Yard argued that the IPT should hear a case brought by women who said they were duped into sexual relationships with undercover police, Dyson ruled that part of the claim should be heard by the tribunal and that part should continue at the high court.

"There is no guarantee," he said, "that the procedures adopted by the IPT in any particular case will satisfy the common law requirements of natural justice."

There was also implied criticism of the IPT in the government's Justice and Security green paper that paved the way for the highly controversial secret justice law which came into effect last year. The green paper said that if the tribunal's remit were to expand, its mechanisms and rules would need to be amended in order to ensure it complied with the European convention, reserving the right to a fair trial.

Nick Pickles, director of Big Brother Watch, describes the IPT as "addicted to secrecy" and says it has long passed the point of being a credible avenue of redress.

"Justice is not being done, let alone being seen to be done," he said. "The IPT is symbolic of the entire system of oversight that has failed to properly inform parliament or the public about how surveillance has been massively expanded because the law has failed to keep pace with technology."

Kat Craig, of the legal charity Reprieve, said: "It has long been clear that proceedings in this quasi-court are tilted in favour of the government to an absurd extent – not only are the vast majority of hearings held in secret, but often the person bringing the complaint will not even be told that they are taking place.

"Now welearn that the IPT is based in the Home Office – the very same building as Theresa May, who has responsibility for MI5. This will only strengthen concerns that the IPT is too close to the very agencies which it is meant to be overseeing."

There is no legal aid for individuals lodging complaints with the IPT. If they hire lawyers at their own expense, those lawyers will not be permitted to attend hearings, other than the small number that are not closed, which are held at court buildings in central London.

There are very often no oral hearings at all. A number of the eight-strong panel of senior lawyers who sit on the IPT will meet and reach a decision on the basis of documents provided by the agencies or whichever public body is the subject of the complaint.

No complaint against any of the intelligence agencies has ever been upheld. On the rare occasions that a complaint against another public body has been upheld, the IPT has sometimes ordered the payment of a small sum as compensation, but no costs.

Some complainants are found not to be under surveillance, while others are being spied upon, but the IPT concludes that it is lawful. On neither occasions are the complainants told of the outcome, in order to conceal evidence of lawful surveillance operations. Instead, they receive a letter simply stating: "No determination has been made in your favour."

There is no right of appeal. And, not only are complainants and their lawyers prevented from being present at the court: until now they have not been permitted to know where the court is located.

The IPT uses a PO Box number and a post code that causes its mail to be sent to a Royal Mail sorting office in south London before being forwarded to its secretariat. However, that four strong secretariat is based at the Home Office, which funds its £296,000 annual budget.

The senior member of the secretariat is an individual who is thought to have previously served as a member of the Home Office's covert investigation policy team before joining another directorate of the Home Office, the Office for Security and Counter-Terrorism.

This person declined to answer questions about his background, and maintained that the tribunal's location was kept secret because members of staff had received "death threats".

However, the IPT would not explain why its location has been concealed since it was established, before any such threats could have been made. Nor would it explain how its staff could be at risk when they work within the Home Office – one of the most secure government departments in Whitehall – and when no member of the public knew what they look like.

The IPT would not meet the Guardian, and instead answered questions by email. The tribunal's website asserts that it is independent of government.

Informed that it was known to be operating from within the Home Office, the tribunal insisted that it remained "operationally independent" of that department and the rest of Whitehall.

As a consequence of the secrecy surrounding the tribunal and the perception that it is unfair, many would-be complainants spurn it.

Few of the individuals who complained that the UK's intelligence agencies were involved in their so-called rendition and torture in the years after 9/11 have turned to the IPT, for example. Instead, many sued in the civil courts, and settled for damages.

Among the few victims of so-called rendition who have turned to the IPT are the former Libyan dissident Abdel Hakim Belhaj and his wife, Fatima Bouchar, who were abducted in Thailand in 2004 and flown to one of Muammar Gaddafi's jails. Documents discovered during the Libyan revolution show that MI6 and the CIA co-operated to secure the couple's abduction.

Although the couple is now suing MI6 and MI5 – and also Jack Straw, the former foreign secretary, and Sir Mark Allen, the former head of counter-terrorism at MI6 – they have also brought a complaint to the IPT.

The couple allege that their privileged communications with their legal team in London must have been spied upon during the GCHQ bulk surveillance operations that were disclosed by Edward Snowden.

Two public hearings were held in that case, after the couple's lawyers threatened to seek a judicial review of the tribunal's actions on discovering that a hearing to consider the matter had been held without their knowledge. The case resulted in the agencies giving an undertaking that any intercepted communications would not be used in preparing a defence against the couple's damages claim.

Shaker Aamer, the former British resident who has been held at Guantánamo for almost 12 years has also complained to the IPT. His lawyers say they do not know whether there have been any hearings about his case or not.

In addition, almost a dozen civil rights groups have lodged a complaint with the IPT about the UK and US governments' bulk surveillance operations.