Former home secretary Alan Johnson - an ex-union leader - warned against "petty retribution" in the wake of Ed Miliband's party reform pledge.
"We can no longer go on living the lie with these millions of people signed up as levy-paying members to the Labour Party, and treated as if they were members," Mr Johnson told BBC Radio 4's The World At One.
"I call them the ghosts in the machine. That is bad for the party, it is bad for the trade unions."
The former Communication Workers Union chief added, "I just hope this is not a piece of petty retribution by a trade union."
Shadow Treasury secretary Rachel Reeves said she was "confident" more trade union members would sign up to the party when automatic affiliation is stopped.
"Of course we welcome the support that we get from the trade unions but this is a decision for the GMB," she told BBC Radio 4's Today.
"Since the last general election, membership in my constituency party in Leeds West has increased by 50 per cent. We've got more members, more trade union activists getting involved in the party because they like what Ed Miliband has to say.
"So I am confident that more people will sign up, get involved in the Labour Party, and come out campaigning. But that openness and transparency is really important and that is what Ed is trying to do."
The GMB union is to reduce its spending on Labour Party campaigns and initiatives. It comes as the union announced it was to cut its affiliation funds in the wake of the row over party reforms.
The decision follows plans by Ed Miliband to give individual union members the choice of opting to join the party rather than being automatically affiliated. The union has affiliated 420,000 of its members to Labour but that figure will be cut to 50,000 from January.
GMB CEC expressed considerable regret about the apparent lack of understanding the proposal mooted by Ed Miliband will have on the collective nature of trade union engagement with the Labour Party.
A further source of considerable regret to the CEC is that the party that had been formed to represent the interest of working people in this country intends to end collective engagement of trade unions in the party they helped to form.
The CEC also decided to scale down by one third the level of its national political fund.
The GMB union's general secretary has criticised the language used by some within the Labour Party about trade unions, claiming it was "very disappointing and insulting".
Paul Kenny predicted just 10% of GMB members affiliated to the Labour Party would retain that status under the new system proposed by Ed Miliband.
Mr Kenny told BBC Radio 4's Today programme: "I anticipate we will now have to ballot our members so that we can comply with what Ed wants.
"I think we will be lucky if 10% of our current affiliation levels say yes they want to be members of the Labour Party, because they are two different things - campaigning for issues with the Labour Party and being members of the Labour Party are two entirely different things".
Mr Kenny added: "We have been trying to encourage our members to join the Labour Party for a very long time, in our magazines, in meetings, at our conferences. I have to say we have not been knocked down in the rush".