The building industry watchdog is investigating the construction union's disruption of five major Sydney sites over safety issues, including claims that toilets were blocked at a major CBD site.

The Construction, Forestry, Maritime, Mining and Energy Union NSW has been targeting Watpac and Probuild as part of a safety blitz that was behind several work stoppages over the past week, at the same time as it ramps up pressure on the two builders to sign up to its new industry agreement.