Two discs containing documents about the Mark Duggan, Azelle Rodney and Robert Hamill inquiries have been lost since early January.
In a statement, the Ministry of Justice (MoJ) said it had launched an investigation in to the security breach, which is against its guidelines.
The families of the three men have been informed, the MoJ said, adding that immediate steps had been taken to locate the discs, although they have not yet been found.
Police officers involved in the inquiries have been warned information about them could reach the public, as lawyers are undertaking a review of the missing documents to discover if they held confidential or sensitive details.
The police marksman who killed Mr Duggan and the identities of other officers involved have never been made public.
A spokesperson said: “At this stage there is no evidence to indicate that the information loss arose from malicious intent.
“As well as safeguarding individuals’ interests, the government has undertaken urgent investigations into how this incident was able to happen, and further investigations continue in relation to both the conduct of individuals and the organisational safeguards against information security breaches of this kind.
“A member of staff has been suspended to facilitate the investigation. Once concluded disciplinary action will be taken if appropriate.
“As part of this, an independent review has been commissioned to look at all the circumstances of this loss and identify lessons learned.”