A former undercover police officer who has become a whistleblower has joined a boycott of a public inquiry into the covert infiltration of political groups, saying it was concealing the state’s misconduct.

Victims of the undercover spying had previously walked out of the inquiry, criticising the judge leading it for allowing too much of it to be cloaked in secrecy.

On Wednesday, Peter Francis, a key figure in the controversy over the police’s use of undercover officers whose revelations had helped to force the government to set up the inquiry, boycotted its latest hearing.

He told the judge, Sir John Mitting, that his decisions giving anonymity to police spies undermined the ability of the inquiry to uncover the truth of how the police had infiltrated more than 1,000 political groups since 1968.

Francis has argued at previous hearings of the inquiry for the fake names of the undercover officers to be published.

But he said Mitting had accepted on many occasions applications from undercover officers to have their identities concealed “wholesale, with minimal, obfuscatory or no reasoning provided at all”. He added that he did not want to spend more public money submitting arguments that were unlikely to change Mitting’s approach.

“Without meaningful disclosure, neither I nor, more importantly perhaps, the victims of undercover policing will be able to properly question the evidence put forward by the police officers during the evidential stage of the inquiry.

“This is crucially important, particularly when the inquiry must remember that these former police officers have been trained to lie. It was a fundamental part of their job.

“Without cover names being released, so many victims of undercover policing will never even know they were targeted. Such an outcome is the very opposite of the professed aim of the inquiry, which is primarily to establish the truth.”

Francis was sent by his superiors to infiltrate anti-racist groups for four years in the 1990s. However, he later blew the whistle on the activities of his covert unit, the Special Demonstration Squad, becoming a crucial source for the Guardian.

In 2013 he revealed how he and colleagues had secretly gathered information on the campaign run by the family of murdered teenager Stephen Lawrence to compel the police to investigate the racist attack properly.

The revelations, coupled with other disclosures such as the frequent deception of women into intimate relationships by the police spies, compelled Theresa May, when she was home secretary, to set up the public inquiry in 2014 to examine the misconduct of the undercover officers.

However, the £10m inquiry, despite being scheduled to be completed this year, has yet to hear any evidence in public. The delay has been caused by voluminous legal applications from the police to keep secret the identities of individual undercover officers.

The latest hearing, on Wednesday, lasted six minutes as neither the victims, nor Francis, were present in the courtroom to oppose the latest tranche of applications from the police. There was a protest outside.

The victims and Francis have not taken the decision to abandon the inquiry completely.