Nine chief executive Hugh Marks has resigned after five years in the top job, saying it is time for him to "begin the process of moving on".

Mr Marks oversaw the Nine network's merger with Fairfax in 2019, the biggest shake-up of Australian media in decades.

The entity owns free-to-air Nine Network, The Sydney Morning Herald, The Age, The Australian Financial Review, a majority stake in Domain, streaming service Stan and a 54.5 per cent stake in radio network Macquarie Media.

It is also led by Peter Costello, the chief executive and chairman of Nine Entertainment.

Mr Marks made the announcement in an email to staff across the network in television, radio and print on Saturday afternoon, and thanked them for their work.

"After five successful years for Nine, I have decided the time is right for me begin the process of moving on," the email said.

"It is the ingenuity, creativity and dedication that you all bring to Nine and the Nine family which makes this place special, and which will ensure it continues to lead the market for many years to come.

"COVID-19 has also demonstrated how we are stronger together."

He said he would make an announcement about this departure to the market on Monday, and the process of replacing him would begin then.

"I will be around to ensure a smooth transition as the business embarks on its next stage of growth," he said.

In the email, the CEO reflected on the enormous changes to the business and the difficulties faced by the company during the COVID-19 pandemic. 

"We have gone from being three separate, legacy media businesses in Nine, Fairfax Media and Macquarie Media, each with their own structural challenges," he wrote.

"… and created a business that now has a diversified revenue base across both advertising and subscription, and that has a clear growth strategy for decades to come."

Nine is reporting that Mr Marks' departure follows the company's AGM on Thursday.

Fairfax shareholders overwhelmingly backed Nine Entertainment's takeover at a meeting in late 2018, after the Australian Competition and Consumer Commission (ACCC) approved it.