Electricians working on the project say the firm has failed to follow agreed consultation procedures over the lay-offs and did not implement the traditional "last in, first out" procedure.
They say the firm is targeting individual workers, including an AEEU safety representative who has been critical of standards on the project.
In April, Balfour Kilpatrick drafted in 40 electricians from other sites in a bid to keep the project on schedule following an overtime ban by electricians.
A Balfour Kilpatrick spokeswoman confirmed that redundancies were scheduled to begin on the controversial project within the next four to six weeks, but declined to comment further. She said Balfour had followed correct consultation procedures.
An AEEU source said the union was "very unhappy" at Balfour Kilpatrick's actions, adding that the union would take the firm to an industrial tribunal.
The opera house has been the subject of several safety scares, and electricians have staged a number of unofficial walk-outs in protest at safety standards.
In December, a 3 tonne crane that was situated on the roof of the James Street building toppled over. It was prevented from falling on to the busy piazza below only because it became wedged on scaffolding erected alongside the building.
The workers, who were notified on Wednesday, will be laid off on Friday and will receive two weeks' pay in lieu of notice. Eight have been given work on other sites.
UCATT says the worker was victimised because he compiled a report criticising safety standards on the site.
The worker, a UCATT member employed by subcontractor Cinnamond Contracts, was appointed safety representative after a labourer was injured falling from an unprotected platform.
But a spokesman for Schal said: "Schal is doing everything possible to promote safe working practices and to improve safety generally on the project. However, the appointment of safety representatives is the responsibility of the union and individual contractors.
"Cinnamond Contracts' package of works is running down and we understand that the proposed union safety representative, who is employed through the agency, will shortly not be required on the project." He added: "There was a scare [with an overturned truck] and the working methods have been changed."