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MacDonald has been in the news recently over a helicopter trip to the Bay of Islands and receiving a bonus and pay rise of $82,500 in the past year to take his salary to about $645,000.
The salary hike, consisting of a 2 per cent pay rise and the rest a bonus, was approved by the board.
The helicopter trip was picked up by the Serious Fraud Office investigating fraud claims by mayoral candidate John Tamihere over the sale of the council's Civic Administration Building to Civic Lane Ltd, which is owned by Tawera Group's chief financial officer, John Love.
The SFO cleared Panuku of any wrongdoing over the $3 million sale but raised concerns about a potential conflict of interest involving MacDonald, saying acceping the flight "was ill-advised".
Young-Cooper, who was not chairwoman at the time of the helicopter trip in January 2017, said MacDonald had followed the correct procedure. MacDonald also hit the news after papers released to the Herald under the Official Information Act showed Tawera Group chairman Mike Mahoney wrote to him expressing an interest in developing the historic Vos boat shed on council land at Wynyard Quarter managed by Panuku.
Young-Cooper said no decisions have been made as to how the Vos boat yard is going to be run and managed.
"There are several parties who have expressed an interest over the years and Mahoney is one of them," she said.
The Herald is seeking comment from MacDonald.
He joined Panuku in November 2016 as chief executive after working in West Africa, Abu Dhabi, Dubai and London for the past 10 years.