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This comes amid a number of rumours swirling around the impending departure of the boss in recent weeks - and an earlier firm denial to NZME that he was leaving shortly.
MediaWorks owns television and radio assets, including TV station Three and radio brands The Edge and The Rock.
"I have absolutely loved the experience of leading this exceptional company over the past four years and it has been a privilege to do so," said Anderson in a statement, confirming he would depart at the end of the year.
"When I joined MediaWorks back in October 2016, my focus was to bring stability to a company that had been through years of turmoil and to get all arms of the business into a position where they would be sustainable and competitive in their own right.
"Fast forward to now and we have welcomed QMS into our family and alongside our radio business, they have come together into one building that allows collaboration across our brands."
His departure comes with the future of the company's TV arm still up in the air.
"Things are also looking positive for the sale of TV and we hope to make an announcement in the coming weeks," he said.
The latest financial result from MediaWorks showed that the company had slumped to $25.14 million loss.
The loss was largely attributable to an impairment of $21m, including a $12.13m write down on property, plant and equipment assets.
Financial statements for the year to December 2019 report the company's total liabilities more than doubled during the year to $296.34m ($138m in 2018) with borrowings of $133.1m at balance date.
The impact of Covid-19 has severely impacted the business.
MediaWorks had obtained $8.6m of wage subsidies and had asked all existing employees to take a voluntary 15 per cent pay cut.
Full salaries were, however, reinstated at the beginning of July.
The company also announced last month that 130 staff were being made redundant in its radio and sales teams.
"Covid-19 has simultaneously changed the world and impacted our business in ways that we could not predict or prepare for," Anderson said earlier.
"It has also completely changed the market that we operate in and this means that we must adapt to ensure our survival and sustainability in the coming months.
"... we must begin reducing the size of our business and we are now entering a restructuring process across our sales, out-of-home and radio divisions. MediaWorks needs to be a different shaped business to operate in a different world."