The demotion was a result of a performance review process with several senior staff in October.
Mr Bowcott became involved in the V8 series in 2008 after being promoted to deputy chief executive under then chief executive Michael Redman.
"Once the V8 audit came out obviously there was criticism of the governance, particularly criticism of Michael and other management shortfalls there," Mr Harris said.
" I'm confident in his capabilities to fill the general manager role. Blair is obviously disappointed but understands the importance of him taking a level of responsibility."
Mr Bowcott last night declined to comment and referred questions to Mr Harris.
But he previously rejected calls from his former boss to follow his lead and quit, saying he was just following his boss' orders.
Mr Redman resigned from his role as chief executive of Auckland Council's Tourism Events and Economic Development business the day after the report was released.
Mr Harris said he had focused on speaking to senior leaders about his expectations as he addressed criticism of the council made in the V8 audit.
But he had no plans to make any further job changes.
"My focus has been on the senior leadership and the importance of collective irresponsibility in these areas."
The council had also started addressing criticisms in Audit New Zealand's annual report on the council's processes, issued last week.
Mr Harris, who took up his position in April, believes best practice processes may have been sidelined as council focused on achieving its vision, to become an events city.
"I suspect the council was focused on some visionary achievements for the city, and sometimes when you do that you can lose focus of the day to day running of an organisation."
The role of deputy chief executive will be disestablished and shared among the council's seven general managers when required, as it was before the role was established in 2007.
At the time Mr Redman said having a permanent person as deputy CEO would ensure "consistency of knowledge and process".