A unionist will face court for allegedly organising a strike at a Perth construction site after being told workers' pay would be docked for attending a meeting during work.

Fair Work Building and Construction has launched legal proceedings against CFMEU assistant state secretary Joe McDonald and 49 employees who were involved in the industrial action in May.

It is alleged that McDonald and two other CFMEU officials held a pre-work meeting with workers on the Lakeside Joondalup Redevelopment project that ran into work time, and when the head contractor lawfully docked four hours of pay, McDonald organised a vote that resulted in a walk-off.

The maximum penalties are $10,200 for an individual and $51,000 for a union per breach.