The move follows a series of safety concerns that have rocked the project since the death of Patrick O'Sullivan, an operative for concrete firm PC Harrington, earlier this year.
Union officials from UCATT and T&G are angry that their safety induction training has been snubbed by the company.
The unions feel particularly aggrieved as they use the safety meetings to recruit members.
Despite the anger, Multiplex said that the change in safety induction training had no hidden agenda. A Multiplex spokesman said: "Safety training is carried out on a rota basis. The unions carry out the training for a period of time and the company then carries out the training for a period of time and the unions are well aware of that."
A site source told Building that Multiplex notified unions of its decision less than a week after a memorial march for O'Sullivan had taken place last month.
He said: "As a worker has died on the project, the issue of safety is very sensitive across the site."
The source added that it was felt on site that Multiplex was trying to reassert its authority following April's march, which was attended by several hundred workers.
The timing of Multiplex’s decision has been awful
Wembley site source
He said: "The timing of Multiplex's decision to take control of safety has been awful. The move has been seen as Multiplex hitting back at the workforce and site representation."
UCATT general secretary George Brumwell said: "We take exception to any slur on our trainers. And if any feelings have been hurt due to the memorial march, this is not the way to progress."
T&G regional organiser Alan Bricklejack said there was a meeting between the unions and Multiplex last Friday.
He said: "We are currently in discussion with Multiplex over the issue and hope to resolve it as quickly as possible."
In February, Building revealed that quantity surveyors employed by Multiplex had warned the company's directors last August – five months prior to Patrick O'Sullivan's death – that they had "serious safety concerns" about PC Harrington.
However, Multiplex said at the time that the QSs were unqualified to comment on safety, that it had confidence in the records of all its contractors and that PC Harrington had its "unequivocal support".
Police and the Health and Safety Executive are continuing a joint investigation into the accident.