The Unite general secretary spoke out in the wake of allegations, which his union has since been cleared of, that it interfered with the choice of the party's candidate in the seat.
Giving the Jimmy Reid Memorial Lecture in Glasgow last night, Mr McCluskey said: "The union-Labour link is a question of principle.
"It is not about how Labour funds itself. It is about how democratic we are as a society, about whether the formal equality of capitalist society can ever become a real equality.
"So that is why I am up for the debate about how to improve and develop the way trade unions and the Labour Party work together.
He added that he could not come to Scotland without pointing out the "debate arose out of disgraceful attacks by the right-wing on my union and its activists in Falkirk."
Labour has been in dispute with Unite after it recruited around 100 new members in a bid to help secure the nomination for its favoured candidate. Leader Ed Miliband has proposed far-reaching reforms of its links to the unions.