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Former British intelligence officer Ian Hurst - also known as Martin Ingram - claimed the murders were "authorised by Northern Command" and "Mr McGuinness was OC Northern Command".
Sinn Fein said Mr McGuinness totally rejected the allegations, saying they were "more lies from an individual with a highly dubious track record".
The spokesman added: "Judge Smithwick has already been critical of the quality and nature of the evidence provided to his tribunal by the British state.
"This individual, who uses a variety of names including Martin Ingram, has no credibility. By his own admission he is part of a British security apparatus which played a very negative and malign role in the conflict.
Ch Supt Harry Breen and Supt Bob Buchanan were killed in 1989
"He has also become the source of many untrue tabloid stories about Martin McGuinness and other Sinn Fein leaders.
"His submission to the tribunal needs to be seen and judged in that context."
However, the claims prompted expressions of concern from the DUP's Gregory Campbell, Ulster Unionist leader Mike Nesbitt and the TUV's Jim Allister.
Mr Hurst gave evidence to the tribunal investigating allegations of Garda/IRA collusion in private session last week.
His evidence was read at the tribunal on Tuesday, with some slight redactions.
The operation to kill the officers was known as a "spectacular" and would have needed political cover, he said.
Intelligence documents
The two RUC officers were ambushed returning from a meeting in Dundalk Garda Station in March 1989.
Mr Hurst told the tribunal: "My understanding was that they were going to abduct them and interrogate them using extreme violence."
He said the plan was to get paperwork they were believed to be carrying then kill them.
Between 30 and 60 people would have been involved in the operation, and four or five of them could "reasonably be expected" to have been working as agents, Mr Hurst said.
The former intelligence officer also said that Freddie Scappaticci was the highly-valued agent known as Stakeknife, whom he described as "the most skilled investigator of suspected informers" within the IRA and one of their executioners.
He also claimed that he had seen intelligence documents linking two Garda members with the leaking of information to the Provisional IRA.
Mr Hurst said he had seen Owen Corrigan described on intelligence documents as a "rogue" garda.
References to Mr Corrigan would have occurred up to 10 times over a period of three years, while he saw the name of former garda Leo Colton referred to once or twice.
Both men deny the allegations against them.
Last week, the press and public were excluded from the tribunal while it heard evidence from Mr Hurst.
Senior counsel for the tribunal, Mary Laverty, said the move was necessary to protect "life, limb or state security".
The tribunal was established in 2005 to investigate allegations of Garda collusion in the murders of RUC Chief Superintendent Harry Breen and RUC Superintendent Robert Buchanan.
