The MoJ said last week that two discs relating to inquiries into the deaths of Azelle Rodney, Mark Duggan and Robert Hamill went missing in early January.
All three men were killed either at the hands of the police or in circumstances sparking accusations of police collusion.
Their deaths led to outcry, and officials were forced to set up judge-led inquiries to probe the killings.
Cops say they have taken “necessary steps” to ensure the protection of any officers named in the documents. Family members of the men are outraged.
Mark Duggan was shot by police in 2011.
His aunt Carole Duggan said, “The criminal justice system went out of its way to protect the identities of the officers who killed Mark, issuing all manner of reporting restrictions and anonymity orders in court.
“Now we learn that this apparently sensitive information has been ‘lost in the post’ at the Ministry of Justice.
“How did this file go missing? And why? Scotland Yard and the ministry have questions to answer if we are ever going to get to the bottom of why Mark was shot dead while unarmed and surrendering to police.”
Robert Hamill was beaten to death by a loyalist mob in Portadown, Northern Ireland, in 1997. His death was referred to an inquiry after claims of security forces collusion.
His family said they were “dismayed” at the loss of the discs.
Azelle Rodney was shot by police in 2005.
A police marksman only known as E7 is due to stand trial for his murder.
Azelle’s mother Susan Alexander said the loss of the files was “shocking news and very disappointing”.
She added, “My lawyers are in contact with the Ministry of Justice on my behalf to establish exactly what data from the case —and particularly that relates personally to me—is on the discs that have gone missing.”