My organisation is proposing workplace change that is permitted by a modern award, but is still likely to have a significant effect on employees covered by the award, do I have to comply with the consultation procedure in that award?

No. Where the award makes provision for alteration of any of these matters an alteration is deemed not to have significant effect. For example, under the Clerks-Private Sector Award the employer can change the days on which a part-time employee works by giving one week’s notice of the change (clause 11.4).