The high-profile businessman has had name suppression since he was charged in February but that order lapsed yesterday.
At a hearing in May, Heart of the City's board supported Swney's bid to keep his identity secret.
Chairman Terry Gould said yesterday that Swney's contract was terminated last week after Mr Gould received new information about the alleged offending.
"It has transpired since then that at the time we were misinformed, if not deceived," he said.
"Clearly, if we knew then what we know now, the decision [to support the name suppression bid] would have been different."
Mr Gould said he was only told the details of the allegations during a "difficult conversation" between the pair 10 days ago.
Much of the allegations relate to non-filing of income tax and GST returns.
The IRD investigation was sparked in September, 2011 during a routine review of a GST refund claimed by the organisation.
The number on the invoice did not match that of the listed company and a wider inquiry began into Swney's financial affairs.
An IRD summary of facts alleged the defendant admitted to falsifying the invoice, and more digging found further fictitious invoices in the names of other companies including the New Zealand Herald.
The IRD claimed those invoices linked to one of several bank accounts shared by Swney and his partner Ange Marshall.
Court documents alleged Swney attempted to address his finances once he knew he was being investigated, filing tax returns covering nearly 13 years in November 2012.
Criminal charges were laid 15 months later.
Members of the family were at Swney's Ponsonby home yesterday but did not open the door.
Heart of the City - which collaborated on the Auckland Tourism, Events and Economic Development-developed "The Show Never Stops" marketing campaign and events like Artweek Auckland - last year received more than $4.2 million from Auckland Council, which came up with about 80 per cent of the organisation's funding.
The figure has risen steadily since 2008 when it received $2.8 million.
Auckland Council would not comment on whether future funding would be jeopardised but welcomed the organisation's decision to seek a new chief executive and bring in forensic accountants.
Mr Gould was quick to back Heart of the City's 15 other employees and poured cold water on any suggestion of job losses.
"It is much bigger than just one man. It does incredibly important work in the context of Auckland," he said.
Swney will be back in court in November.
The charges, laid under the Tax Administration Act, attract a maximum penalty of five years imprisonment and/or a fine of $50,000.
