Hundreds of Home Office files on a secret undercover police unit appear to have been lost or destroyed.

Theresa May’s department has not handed a single document about its role in setting up and financing the Special Demonstration Squad (SDS) to Operation Herne, the long-running police investigation into the unit’s activities, or to the independent legal review led by Mark Ellison, QC.

The situation echoes the 114 files on historical child abuse that the department admitted had been “lost or destroyed”. Its inability to find the latest batch of documents is potentially more embarrassing because the home secretary has previously criticised the poor state of records on the unit.

At the publication of the Ellison Review, which was fiercely critical of the SDS and the lack of control by Scotland Yard, Mrs May said there was “real concern” over Metropolitan police record-keeping and referred to the alleged “mass shredding” of evidence in 2003.

The squad has been the focus of scrutiny after revelations that officers used dead children’s names to create identities, were deployed in political protest groups and had long-term relationships with female activists, sometimes marrying and fathering children.

Although run from Scotland Yard, the SDS was created in 1968, when James Callaghan was home secretary, in response to the Vietnam war protests outside the American embassy in London. The Home Office financed it directly and its hand-picked members were trained by MI5. An external review was set up to report on the Home Office’s involvement in the unit, but it is understood that no papers have been made available to either the police investigation into the SDS or to Mr Ellison’s review.

A source with knowledge of the reviews said: “The police took a hammering over poor record-keeping and loss of documents, but it turns out the Home Office is far, far worse.”

The Met has continued to find and hand over thousands of files to the police investigation into the SDS. The Met has also interviewed 85 people regarding the allegation of “mass shredding” but said that only one person remembered the incident. That witness claimed that four bin bags of papers were destroyed in 2001 after the information was computerised.

The Met has appointed an assistant commissioner to head the trawl for documents before a promised public inquiry into the SDS, particularly the deployment of officers in groups involved in the campaign for an investigation into the murder of Stephen Lawrence. The Ellison Review found evidence of a “spy in the camp” who reported back to Scotland Yard on the Lawrence family.

The SDS was disbanded in 2008, and undercover deployments are now overseen by the Surveillance Commissioner. A Home Office spokesman would not comment on the loss of documents. He said: “In the interests of transparency, the home secretary announced in March that the permanent secretary would commission a forensic external review in order to establish the full extent of the Home Office’s knowledge of the SDS so we could understand the role the department played.”

A Met assistant commissioner, Martin Hewitt, acknowledged the force’s failings: “With the amount of information generated in everyday policing, effective record management can present challenges and the Met fully accepts that it has not kept good records of what was retained or destroyed in the past.”