Owen's last day in the mayor's office will be April 23. She is taking a new job as chief sustainability adviser at the Department of Conservation.
Foster said in a statement that Owen's resignation was "obviously sad news" for him.
"But I recognise the fantastic opportunity that exists within her future role. One that will have national significance and speaks to her passion for the environment."
He said Owen came on board during the Covid-19 pandemic during challenging times for the city and New Zealand.
"She has worked tirelessly to establish a Mayor's Office that manages and engages with the diverse and complicated issues that face a capital city in an era of considerable challenges."
It has previously proven difficult to find staff for Foster's office.
In May last year the Herald reported it appeared the council was having a tough time finding someone to bridge the gap between Foster and the media, for example.
The council first advertised the role of public affairs adviser to the mayor in November 2019, although an experienced contractor filled the position in the meantime before joining the Ministry of Health as a senior adviser.
That role continued to be advertised on more than one occasion and recruitment agencies shoulder-tapped several individuals, only to draw a blank.
John Bullock was eventually hired as a media adviser and remains in the role.
