The security service MI5 wiped secret information from computer hard drives being held by an inquiry examining the murder of solicitor Pat Finucane.
Retired Canadian Judge Peter Cory, head of the inquiry, complained to police and feared a diplomatic incident.
In 2004, he recommended a public inquiry into the killing, but one has yet to be held.
Mr Finucane’s family believes state collusion in his murder went to the top of government.
The prominent solicitor was shot dead by loyalists at his home in north Belfast in 1989.
Details of a visit by MI5 to Judge Cory’s London offices in 2002 – corroborated by the inquiry’s senior counsel – are contained in a BBC Spotlight programme.
MI5 told his staff they were removing all the inquiry’s hard drives in the interests of national security.
They were erased before being returned.
BBC Spotlight was told MI5 was concerned the inquiry’s computer system was insecure and a leak could expose the identities of informers.
Judge Cory raised MI5’s intervention with the Commissioner of the Metropolitan Police, Sir John Stevens, but decided against pursuing the matter to prevent a diplomatic incident.
The judge had printed back-up copies of the material and believes nothing was ultimately lost.
‘Cabinet eyes only’
Mr Finucane’s widow, Geraldine, said: “I was told that papers marked ‘cabinet eyes only’ involved the collusion and the killing of my husband.
“There is something there that needs to be exposed,” she told the programme.
BBC Spotlight also reveals that the late Willie Frazer, the campaigner for victims of republican violence, had a role in distributing weapons to loyalist paramilitary groups.
The automatic rifles had been brought into Northern Ireland from South Africa in 1987 by Ulster Resistance, a group formed to oppose the Anglo-Irish Agreement.
The weapons were used to murder at least 70 people.
A police report on the activities of the former UDA boss Johnny Adair states he was receiving weapons from Ulster Resistance in the early 1990s.
His contact in Ulster Resistance was Willie Frazer.
Spotlight on The Troubles: A Secret History continues on Tuesday at 21:00 BST on BBC One NI and BBC Four.