An undercover police officer who infiltrated anti-racist groups has called for a full public inquiry into controversial police operations that have spied on the protest movement for more than four decades.

The call from Pete Black comes as Britain's most senior police chief, Bernard Hogan-Howe, faces questions on Thursday about whether two undercover officers – Bob Lambert and Jim Boyling – appeared in court using their fictional identities as political activists.

Black worked alongside Lambert and Boyling in the 1990s in the covert Special Demonstration Squad (SDS), part of the Met's Special Branch.

Its activities – gathering intelligence and disrupting the activities of political campaigners – were later transferred to the control of the Association of Chief Police Officers, which maintained a network of spies in protest groups until last year. The unit has since been returned to the Met.

Nine separate inquiries have been launched this year into the controversy surrounding undercover infiltration of political groups. They include disciplinary inquiries, a review by a senior judge and investigations by official police watchdogs.

Black said the home secretary, Theresa May, should now open a full public inquiry and recognise that the alleged abuses of power were not isolated incidents but were widespread and approved by senior police officers.

He said, for example, that senior police officers had claimed their agents were not permitted to have sexual relationships with activists. Black said, however, that superiors knew officers had developed sexual relationships with protesters to give credibility to their cover story and help gather evidence.

Of the seven undercover police officers identified as having infiltrated protest groups, five had sexual relationships as part of their cover, often developing long-term relationships. They include Lambert, Boyling and Black, as well as Mark Kennedy, who was unmasked as a police spy last year.

Black said junior officers should not be made scapegoats or prosecuted for doing what they were authorised to do by their superiors.

Hogan-Howe, the Met police commissioner, conducted an inquiry into police infiltration of protest groups in his prior role at HM Inspectorate of Constabulary. The publication of his report was abandoned last week, hours after the Guardian and BBC Newsnight revealed evidence that undercover officers may have been prosecuted under their false identity.

He will be questioned by his force watchdog, the Metropolitan Police Authority, about the growing controversy surrounding undercover policing. Jenny Jones, a Green member of the MPA, will demand that Hogan-Howe reveals "how many undercover officers have given evidence under a false name, how high up the ladder does the deception go and who authorised this appalling behaviour".

Black said it would be relatively easy to give these answers as the police unit he worked for kept a secret file listing details of the authorised crimes committed by undercover officers during their deployments.

He said undercover officers reported to their superiors any crimes they committed while working under their fake personas. Their senior officers would then give them retrospective authorisation to have committed that crime, he added.

Undercover officers are permitted to participate in criminal acts provided they do not instigate them, as it can help the officer to win the trust of the people he is seeking to infiltrate. But this is a legal grey area as defendants under English law can mount a defence if they can show that an undercover officer acted as an agent provocateur.

Last week the police watchdog, the Independent Police Complaints Commission, started investigating claims that Boyling, a police spy who was embedded in an environmental group, lied under oath about his real identity. The Metropolitan police said it was reviewing similar allegations about the second former undercover officer, Lambert, "with a view to referring it to the IPCC".

Black said a series of IPCC investigations into individual officers would not get to the bottom of what has gone on. He said individuals should be granted the right to give evidence to a public inquiry without fear of being prosecuted.

Since he first went public in March last year, Black has argued that the public should know more about the undercover operations so they can make an informed decision about whether they were necessary. He supports a full inquiry reminiscent of one in the US in the 1970s, known as the Church committee, which uncovered the illegal activities of the American intelligence agencies.

Hogan-Howe appears before the police authority on the 43rd anniversary of the setting-up of the SDS, originally to tackle anti-Vietnam protests.