The programme, made by Central Television, produced a series of witnesses, some of them anonymous, in support of its claim that Mr McGuinness was in charge of the IRA, adding that it was sending its evidence to the police. The RUC said the programme was being studied.
The allegations have given new life to Unionist arguments that Sinn Fein should be banned because it is no more than a front for the IRA. On the programme, Sir John Hermon, former Chief Constable of the RUC, said the two organisations were 'inseparable' and Mr McGuinness had long been 'very central to what is going on'.
Mr McGuinness has been a prominent figure in republican circles for more than two decades.
He and other Sinn Fein figures responded with a series of counter-attacks on the Cook Report, saying it contained lies, innuendo, smears and black propaganda.
'Mr Cook and his colleagues, in producing this programme, cannot distance themselves from the campaign of demonisation which sustains the climate in which our members and their families are being killed,' a Sinn Fein spokesman said.
Mr McGuinness did not appear on the programme, but yesterday gave a series of interviews in which he denied its claims. He told a BBC interviewer that as a young man he 'took up a particular stance which I'm not prepared to elaborate on in this programme'.
Asked if he had ever been a member of the IRA, he replied: 'I'm not stating any opinion at all about what I was in the past. What I'm saying is I'm not a member of the IRA. I'm not chief of staff of the IRA and I'm not Britain's number one terrorist.'
He had consulted legal advisers and been told that bringing a libel action would cost up to pounds 500,000, and it was unlikely any British court would find in his favour.
Ken Maginnis MP, security spokesman for the Ulster Unionist party, said it was important for the Government to take seriously shortcomings in the law which permitted 'the godfathers of terrorism' to remain at large. He called for the introduction of selective internment.