Mr Cannon-Brookes on Monday evening revealed he had taken an 11.28 per cent stake in AGL Energy, via his Galipea Partnership and affiliates, becoming its largest shareholder.
The announcement came just hours after AGL released a letter to shareholders asking them to back a board plan to split the company into two entities - a green energy retailer called AGL Australia and a coal-fired electricity generator called Accel Energy.
The groups have targets to reduce emissions to net zero by 2040 and 2047, respectively.
"We will be voting against the upcoming flawed merger," Mr Cannon-Brookes posted on Twitter on Monday night.
He believes AGL can "benefit massively" from the future decarbonisation of the Australian economy because the transition will require "electrifying everything & moving our grid to be powered by cheaper, reliable renewables".
"The demerger makes no sense, or cents," he tweeted.
"We believe it destroys value for everyone - shareholders, employees, Australia and the planet."
AGL told shareholders the demerger will create the "potential to maximise growth in the value of shares by giving each company the freedom to pursue individual strategies and growth initiatives".
For the demerger to succeed it requires 75 per cent shareholder approval. A vote will take place on June 15.
Earlier this year, Mr Cannon-Brookes launched an unsuccessful takeover bid for AGL worth about $9 billion, plus debt, via a consortium.
The consortium wanted to take the company private, close its coal-fired plants about 10 years earlier and spend $20 billion developing renewable energy and battery storage.
AGL shares closed on Monday at $8.62. The consortium's final offer in March was $8.25 a share.
