Mr Brown said he would be meeting with board chairman Graeme Hawkins and chief executive Tony Gibson in the coming days to seek an explanation after the 100 per cent-owned council company failed to inform him and councillors of the work ahead of recent discussions about a central wharves strategy.
One option in the strategy was to remove Marsden wharf. Others options were to keep it.
Last week, councillors were surprised to learn that council officers had approved consent for the port company for two large wharf extensions into Waitemata Harbour and would need to reclaim 3ha of seabed between them over time.
Mr Brown said he was aware of the extensions. He was not concerned about them.
"Decisions on resource consents are made by council officers not elected officials. This was an application within the existing port precinct for piled structures and the decision was published in the usual way," Mr Brown said of the wharf extensions.
A ports spokesman said the piles will be left in place until it was able to deepen the shipping basin in the area.
Ultimately the expanded shipping basin will be used for ships berthing at Bledisloe Wharf.
"It will mean the port is able to utilise a berth that is currently inaccessible and reduces the need to extend further north
"The work is part of the port's long-term plan to optimise the port layout to improve efficiency and keep reclamation needs to a minimum," the spokesman said.
The council granted consent for the demolition works in May 2012. The ports company plans to seek resource consent for deepening work within the next five years.
Last week, the Herald revealed plans by the port company to build two large wharf extensions into Waitemata Harbour and reclaim 3ha of seabed between them over time.
One councillor opposed to further harbour reclamation, Chris Darby, said: "Massive wharf extensions revealed one week, wharf demolition the next. This outfit operates more like a corporate fiefdom than public entity 100% owned by Aucklanders."
Mr Darby said it appeared the mayor was a week late in asking questions of the port company.
"While he is rightly asking questions of today's announcement he ignores the bombshell dropped on Aucklanders last week when the port company's cunning plan to create massive wharf extensions to facilitate cavernous reclamations was revealed," Mr Darby said.