ACIL was set up at arm's length from the council to protect Ports of Auckland from political interference and ensure it operated along commercial lines.
Goff said this should be protected through an agreed Memorandum of Understanding setting out communication protocols, the board appointment process, clear delineation and a dispute resolution protocol.
In the last financial year, ACIL posted a record profit of $138.2m and paid a dividend of $85.9m to council.
ACIL would reduce the number of CCOs to five - Auckland Transport, Watercare, Auckland Tourism, Events and Economic Development (Ateed), Regional Facilities Auckland and Panuku Development Auckland.
Panuku was established in September 2015 as an urban regeneration agency from the merger of Auckland Council Property Ltd and Waterfront Auckland.
Goff will table his draft 10-year budget at a governing body meeting at 1.30pm today. The 21-strong governing body will make decisions on the proposals next month before public consultation in March next year. The budget will come into effect in July next year.