The removals, which were made in October, came after the commission opened a statutory inquiry into the charity in May. It is the first time the regulator has used such powers to remove members of a charity.
The five crew members, who are all volunteers, have lodged an appeal with the charity tribunal in Northern Ireland.
Lough Neagh Rescue has two stations on the shores of Northern Ireland’s largest lake. It has attended more than 500 emergency situations in its 25-year history.
In August, the commission ordered the removed of Trevor McKee as a trustee of the charity. McKee remains the only person appearing on the CCNI’s list of people removed as a charity trustee. His charity tribunal appeal hearing is scheduled for 24 March.
A spokeswoman for the CCNI said she could not name the five crew members in question, although the regulator might do so when a final report into the investigation is published. She said she could not say when this final report would be available.
The BBC has named and filmed interviews with two of the removed crew members. Robert Orton told the BBC that he understod his dismissal was linked to his being a mason, something he said was "a nonsense". Gregory Burke said: "The charity is not boats and equipment; the charity is the membership"
One non-removed crew member contacted at his day job by Third Sector and who asked not to be named declined to comment and said it was a matter for the commission.
He confirmed that the organisation still had about 35 crew members across its two stations, was in the process of training 15 more for the new Antrim station and would not be directly replacing the removed staff.
Lough Neagh Rescue did not respond to telephone messages left by Third Sector.