His comments came as a senior Tory MP demanded that Labour leader Ed Miliband reopen his party's investigation into the Falkirk candidate selection process.
Priti Patel, a member of Downing Street's policy board, wrote to Mr Miliband after new emails emerged that appear to show the inquiry found indications of forgery, coercion, trickery and manipulation.
It came as Gregor Poynton, who at one time hoped to be a frontrunner in the race to be Labour's candidate in the constituency, reportedly accused former Labour election campaign chief Tom Watson MP of being "involved in it all behind the scenes".
Unite has been embroiled in claims it tried to pack the local party to ensure its favoured candidate was selected to Falkirk in the next General Election. There have also been claims union officials who were involved as key witnesses changed their testimony.
Later, it emerged that Stephen Deans, the Unite official at the centre of the Grangemouth dispute, is to stand down as chairman of the Labour party in Falkirk. It followed a meeting of the constituency party at Camelon Labour Club yesterday, called after Mr Deans resigned from the Grangemouth refinery.
However, Ms Patel wrote to Mr Miliband: "I would urge you to reopen the inquiry into the Falkirk selection and explain why you asked Tom Watson to retain his position as Labour election campaign chief."
The leaked emails reportedly suggest the Labour investigation found "there was no doubt that members were recruited in an attempt to manipulate party processes", "evidence that signatures were forged", and that "individuals have been coerced into signing direct debit forms", while others did not understand what they were signing.
Mr McCluskey hit back at suggestions Unite had rewritten witness statements.
"This idea that Unite has rewritten and evidence from the families has been withdrawn" he said. "The families, which is part of Stevie Deans's family, actually clarified the position - they were the ones that indicated they were being misrepresented."
He also denied Unite had read the changed witness statements but confirmed Mr Deans had been involved in discussions about them.
"I don't deny that at all - it's his family. This is an ordinary, decent family that was suddenly faced with the full weight of the establishment - the police, a forensic solicitor. Of course they spoke to Stevie Deans."
The union insists these issues have already been investigated by the Labour party and Unite was found to have done nothing wrong. It added: "Specifically, Unite entirely denies any involvement in or knowledge of the forging of signatures on application forms or of any documents whatsoever; the coercing of individuals to join the Labour party - however that might be accomplished; the recruitment of individuals to the party without their knowledge or any other breach of Labour party rules. Unite called for an independent public enquiry into what happened in Falkirk, and we remain entirely happy to assist such an inquiry."
Meanwhile, last night it was reported that Lorraine Kane, 61, who triggered the probe into electoral corruption when she said she had been signed up to the Labour Party without her consent, had said she "did not change the testimony".
She added: "I did not change anything. I did not withdraw anything."