"Nobody has ever understood it, and it doesn't say anything about transport," he said of the brand.
Auckland Transport had inherited a large number of "weak and irrelevant sub-brands" and these would be phased out over time.
An existing logo bearing his agency's name next to a pohutukawa emblem generic to all Auckland Council-controlled organisations would, however, remain as a "governance" brand.
But a largely unpublicised "soft launch" of the new operational logo has drawn mixed reviews from transport bloggers and hostility from Auckland Council member Cathy Casey, who sees it as unnecessary and a sign of defiance. "We don't need it," she told the Herald after raising concern at the council's transport committee.
"What we need is to maintain the link between ratepayers' money and the CCOs [council-controlled organisations].
"It gives people the biggest fear, that they are out of control, they are empire-building - that they are building something for them and not for the people of Auckland."
Dr Casey said the council had been forced to rein in another of its organisations, Waterfront Auckland, after that body last year spent $25,000 creating a new blue and red logo minus the required pohutukawa.
Auckland Transport's new logo has been criticised by contributors to the website transportblog.co.nz as being hard to understand.
One said he had yet to work out if it said AV, AN or AT, another thought it too similar to the National Party's logo, and a third claimed that - depending on the light - he could read the words "gay" and "cat" into it.
"It's amazing how you can bugger up two letters, AT," said a fourth.
But others believed the symbolism and association they expected it to build with transport were more important than what the letters meant, and Mr Thomas likened it to the red circle and blue dividing line which symbolises the London Underground.
Auckland Mayor Len Brown indicated acceptance of the new logo, on the understanding it would "sit alongside the pohutukawa, making it clear Auckland Transport is an Auckland Council-controlled company".
"The one thing Auckland doesn't need is a large number of different council logos confusing people," he said. "That's why we have acted to ensure the pohutukawa is the predominant logo across council."
But a half-page advertisement Auckland Transport placed in the Herald last week had a colourless pohutukawa tucked away at the bottom right-hand corner, compared with pride of place given to the new logo at the left-hand top.
Mr Thomas said that although the pohutukawa logo would be used wherever possible, it did not "say anything about movement or transport in Auckland".