The retired judge leading a public inquiry into the conduct of undercover officers who infiltrated political groups has granted anonymity to two-thirds of the police spies who requested it.

Sir John Mitting is heading the inquiry examining how undercover police officers spied on more than 1,000 political groups since 1968, following revelations of misconduct.

An analysis by the Guardian shows that 78 undercover officers applied to have their fake identities concealed while their evidence is heard at the inquiry, and Mitting has ruled in their favour in 50 cases. They will give evidence in private or with their identities hidden.

Mitting has faced fierce criticism from the victims of the surveillance, who argue that undercover officers should have their identities published so the public can recognise them and challenge their evidence.

The victims include women who were deceived into long-term relationships, grieving families such as the parents of the murdered teenager Stephen Lawrence and the relatives of dead children whose identities were stolen by the spies. Many of the infiltrated groups promoted leftwing or progressive causes.

Andrea, a trade union activist who has been granted anonymity by the inquiry as she was deceived into a two-year relationship by an undercover officer, accused Mitting of capitulating too much to police demands.

“Mitting does us, and the public, a great disservice by allowing these police spies to hide behind an establishment-constructed wall of secrecy. Without the fake identities, how will the public ever know that they were abused by these agents of the state?”

In a statement, the inquiry said it aimed to be as open and transparent as possible, but that anonymity was granted for a series of reasons – for example, disclosure could put individuals at “serious risk of injury, or in extreme cases, death, because of the nature of the deployments they have undertaken”, or damage their or their family’s private life in contravention of their human rights.

It added that if these concerns were not addressed, “it would be very likely to have an impact on the willingness of witnesses to provide full evidence to the inquiry, and/or on the quality of that evidence.”

Theresa May, the then home secretary, set up the inquiry in 2014 to investigate what she called “very real and substantial failings” of the undercover police.

The inquiry has cost more than £13m so far and was due to conclude last year, but is far behind schedule. It has yet to hear any evidence in public and is unlikely to do so before next year.

In 2016, police started submitting legal applications to keep secret the identities of the undercover officers, arguing that they needed to protect them from harm and preserve covert techniques. The time taken to process these applications has been a key reason why the inquiry is heavily delayed.

Mitting has so far dealt with the cases of 138 undercover officers, with a small number still to be decided.

Of that total, 50 undercover officers did not apply have their fake identities kept secret. The police say there is no record of the identities used by another 10 undercover officers, so Mitting has not been required to make a decision on their anonymity.

Taken as a whole, just over a third of the 138 undercover officers will have their fake identities hidden. Many of them infiltrated political groups in the 1970s and 1980s, with one as far back as 1968.

Mitting has so far published the fake identities of 51 undercover officers which had not previously been disclosed.

Seventeen undercover officers had previously had their identities exposed following investigations by campaigners who had been infiltrated and the media. Another undercover officer, Peter Francis, identified himself while blowing the whistle.

Police ran two covert squads to infiltrate political groups. Mitting has decided that 13 of the 22 undercover officers in one of the squads – the National Public Intelligence Unit (NPOIU) – will have their fake identities concealed at the inquiry. The NPOIU operated between 1999 and 2010.

Members of the squads adopted new identities to assimilate themselves into the groups during deployments that usually lasted four years.