"I thank Roger for his valuable service to Panuku since late 2016 and wish him all the best in his next endeavours," she said.
MacDonald's 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 "its acceptance was ill-advised".
Young-Cooper, who was not chair at the time of the helicopter trip in January 2017, said MacDonald followed the correct procedure regarding the trip.
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.
Young-Cooper said Panuku's chief operating officer David Rankin will continue acting as chief executive pending the appointment of a new chief executive.
MacDonald joined Panuku in November 2016 as chief executive after working in West Africa, Abu Dhabi, Dubai and London for the past 10 years.