The AGL Energy board on Tuesday dismissed his criticism of the imminent split of the company, saying in a statement to the ASX that the demerger is in the best interests of all shareholders.
The tech mogul's push to more quickly power Australia with renewable energy comes amid a tight election where climate politics is heartfelt by those hit by more severe and frequent floods, storms and fires.
Asked on the campaign trail whether it was embarrassing that a tech billionaire was showing more leadership on emissions, Scott Morrison said his government had a practical plan for net zero by 2050.
"If you allow electricity prices to rise by having unbalanced emissions reduction targets, then the price of all of this goes up," he told reporters.
The Atlassian co-founder tweeted on Monday night he had taken an 11.28 per cent stake in AGL Energy, seeking to influence its future by becoming the largest shareholder and rallying others to his cause.
The intervention came just hours after AGL issued a letter to shareholders asking them to back the plan to split the company into two - an energy retailer called AGL Australia and a coal-fired electricity generator called Accel Energy.
The new entities will have a target to reduce emissions to net zero by 2040 and 2047, respectively, which is too slow for the biggest shareholder.
"We will be voting against the upcoming flawed merger," Mr Cannon-Brookes tweeted.
He believes AGL Energy can "benefit massively" because the economic transition will require "electrifying everything & moving our grid to be powered by cheaper, reliable renewables".
"The demerger makes no sense, or cents.
"We believe it destroys value for everyone - shareholders, employees, Australia and the planet."
AGL said it remains committed to "a responsible transition of Australia's energy system" and plans to split the company by June 30.
For the demerger to succeed, 75 per cent shareholder approval is required when the vote is held on June 15.
"This is a private individual and a private company and it is a matter for the market to decide," a Labor spokesman told AAP.
Mr Cannon-Brookes has launched a website - Keep it together Australia - setting out his case for shareholders to oppose the demerger in the hopes of getting the other 15 per cent or more needed to block the split.
"I'm a big believer in AGL's future and the huge possibilities of the economic transition that we are heading to in terms of decarbonisation."
Asked if rising prices for coal and gas would delay decarbonisation, Mr Cannon-Brookes pointed to higher power bills for households.
"The price of wind and sun hasn't changed at all as a result of instability," he said.
"The problem we have here is the input cost of power.
"If you're running renewable energy then you don't have those price rises, which results in lower prices."
But Queensland LNP Senator Matt Canavan, a pro-coal MP, believes the opposite.
"Mike Cannon-Brooks is great at tech but his policies, if applied to energy, would be an absolute disaster for our country," he told Sky News.
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 ramping up renewable energy and battery storage.
AGL shares were trading at $8.36, down almost three per cent, at 1205 AEST on Tuesday.
The consortium's final offer in March was $8.25 a share, which was rejected by the board.
