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Mr Kirkness (47) has accepted the role of weekday editor at The New Zealand Herald in Auckland.
He will remain at the ODT until August.
Mr Kirkness was appointed ODT editor in 2007.
"I've been lucky enough to have a great job, and whoever replaces me will editorially lead, in my opinion, one of the great newspapers and news companies not just in New Zealand but Australasia," he told staff today.
Sir Julian said a replacement would be announced in due course.