He said he had been influenced by a report by the Office of the Auditor-General saying setting clear expectations of council-controlled organisations (CCOs) should do away with the need for councillor directors.
Goff also said he had significantly increased the scrutiny of CCOs through the new committee structure and received feedback from councillors that the appointments did not improve the flow of information from Auckland Transport to the council.
"There was also concern about the inequity created by these appointments given that appointees earn more than $50,000 in directors' fees a year while other elected representatives who carry out extra duties receive no additional payment," the letter said.
Mike Lee has described the move a "retrograde step", City Vision councillor Cathy Casey has vowed to fight it and new councillor Daniel Newman said the issue is not about an improved flow of information from Auckland Transport back to council.
"This issue is does the council have within it elected membership people who meet or exceed the standard necessary to add to the governance of Auckland Transport.
"In my view, regarding Cr Fletcher and Cr Mike Lee, the answer is absolutely," Newman said in a response to the mayor, copied in to the Herald.
Said Fletcher: "I believe there should be elected representation on the board of Auckland Transport."
Waitakere Ranges Local Board chairwoman and former Auckland councillor Sandra Coney said it was "pathetic" that this was one of the first things Goff had done.
She said Lee and Fletcher, from opposite sides of the political spectrum, were excellent people to have on the board.
"Some councillors and some in AT have been gunning for this for the last 18 months," Coney said.
Councillor Dick Quax said Goff did not have the power of appointments to the Auckland Transport board. The Super City legislation gave the power to the council, he said.
Quax said most of Goff's points in the letter were valid, but he looked forward to the pros and cons being discussed and the council making a decision.
Like Quax, councillor Sharon Stewart wanted the issue discussed at an extraordinary meeting.
"Auckland Transport is such an important issue for the people of Auckland. I think we need to have representation from the governing body at the table and collectively the elected councillors and the mayor should nominate an elected member and vote on who will be the best voice to represent us," Stewart said.
Said councillor John Watson: "I do not support the removal/suspension of councillors from the Auckland Transport board. In my view it is essential to have this councillor presence on this board."
Labour's spokesman of Auckland issues, Phil Twyford, said he had an open mind on the issue.
"I believe Mayor Phil needs to exercise much tougher accountability over the CCOs which have behaved like independent fiefdoms undermining the integration that was supposed to be one of the great benefits of the Super City. I think this is what he plans to do," Twyford said.
When Goff was Leader of the Opposition at the time the Super City was being set up in 2010, he described the CCOs as a "clique of cronies" who would be more important than elected councillors.
"The Government has been too quick to centralise power in the hands of a few, instead of all of Auckland," Goff said in a 2010 speech on 'The Future of Auckland'.