Workers on the Manly Fast Ferry could receive as much as a $1 million in total in back pay following the Fair Work Commission's rejection of their workplace agreement after it found that some workers would have been better off under the award, the CFMMEU has said.

The workplace relations tribunal this week quashed an earlier decision to approve the agreement with NRMA-owned Noorton Pty Ltd, following a challenge by the union covering workers on the ferry, the CFMMEU.

Manly Fast Ferry under fire for failing the BOOT test. Credit:James Brickwood

The Commission found under the agreement that full-time shift workers were being short changed by $136.37 per week and part-timers were being paid $36.32 below the award for a 12-hour week.

Under workplace law, a wage deal must pass the "better off overall test", or the BOOT, meaning it leaves workers better off than they would be under award conditions - which are the basic wage safety net.