A second police spy has said the Home Office was aware that undercover police officers stole the identities of dead children to infiltrate political groups.

Peter Francis, a former undercover officer turned whistleblower, said the Home Office helped the spies by providing false passports in the names of the dead children.

His claim comes as Britain's most senior police officer, Sir Bernard Hogan-Howe, is due to publish a report on Tuesday about the secret use of dead children's identities.

It will be released on the same day that MPs on the home affairs select committee are due to question Mick Creedon, the chief constable who is leading the police investigation into the deployment of undercover officers in protest groups over a 40-year period.

Creedon has already conceded that the theft of the children's identities was "common practice" within a covert special branch unit which operated between 1968 and 2008.

Earlier this month, Bob Lambert, one of the leading spies of the unit, claimed that the technique was "well known at the highest levels of the Home Office".

In a practice criticised by MPs as "ghoulish" and "heartless", undercover spies in the unit, the Special Demonstration Squad (SDS), searched through birth and death certificates to find children who had died at an early age. They then assumed the identity of the child and developed a persona based on that identity when they went undercover for five years or longer.

The spies were issued with fake documents such as passports, driving licences and national insurance numbers in the child's name to further bolster their credibility.

Francis, who infiltrated anti-racist groups from 1993 to 1997, discussed the technique with the head of the SDS because he had reservations about stealing the identity of a four-year-old boy who had died. He did not disclose the name of the SDS head.

"We bounced it around – what were his thoughts, what were my thoughts. It was evident that it was standard practice," Francis said.

The head of the SDS told him the Home Office knew the undercover spies "were using the children", he said, as it gave fake passports to the spies knowing that they were in the names of the dead children.

The SDS was directly funded by the government, which received an annual report on its work for much of its existence.

A Home Office spokesperson said: "We expect the highest standards of professionalism in all aspects of policing. That is why Chief Constable Mick Creedon is leading an IPCC-supervised investigation which will ensure any criminality or misconduct is properly dealt with."

Francis was an important source for the Guardian when the newspaper detailed the technique, dubbed the "jackal run" after Frederick Forsyth's novel The Day of the Jackal, in February.

Speaking then as Pete Black, one of his undercover identities, Francis said he felt he was "stomping on the grave" of the boy whose identity he stole. "A part of me was thinking about how I would feel if someone was taking the names and details of my dead son for something like this," he said at the time.

Last month, he said his superiors had asked him to find "dirt" that could be used to smear the family of Stephen Lawrence, the black teenager who was stabbed to death in a racist attack in 1993.

Lambert went undercover for four years in the 1980s to infiltrate environmental and animal rights groups. He adopted the persona of Bob Robinson, a seven-year-old boy who had died of a congenital heart defect.

Interviewed by Channel Four News this month, Lambert said that at the time he did not "really give pause for thought on the ethical considerations. It was, that's what was done. Let's be under no illusions about the extent to which that was an accepted practice that was well known at the highest levels of the Home Office." Lambert fathered a child with a campaigner while he was undercover.

On Tuesday, Creedon is expected to be questioned by the select committee about whether the police will apologise to the parents whose children's identities were taken. Creedon has said he has taken legal advice on whether the spies who stole the children's identities could be put on trial.