"It should have acknowledged that climate change is real, and we cause it, and it will be messy."
The Intergenerational Report, published every five years, is a snapshot of how Australian society and the economy might look in 40 years, covering aspects such as population size, life expectancy, public spending and budget deficits. The Government used the 2015 report, and its comparisons of three long-term budget scenarios, to criticise Labor.
The opposition called it a "highly political document".
Kruszelnicki told Fairfax Media: "The only reason I agreed to do it [promote the report] is because I was told that it would be independent, bipartisan and non-political.
"If it turns out to have been fiddled with or subject to political interference from one side of politics, I would deeply regret playing any part in it whatsoever."
He said he had received "hate emails, hate [tweets] that I am to blame for the one-quarter of scientists being fired from [the Government's scientific body] CSIRO, that I am to be blamed for somebody's daughter having to pay a huge amount for her education for a science degree".
A spokesman for the Treasurer, Joe Hockey, who released the report, said Kruszelnicki had had "a full draft ... prior to filming".
He also denied that it was political, saying it "presented an opportunity for a discussion on the challenges and opportunities facing our country".
The shadow Treasurer, Chris Bowen, said: "You know Joe Hockey has got it wrong when even the person he paid to sell the Intergenerational Report is rubbishing it.
"There are posters and billboards up across Australia with Dr Karl's face on them, and every one is now a testament to the Treasurer's ineptitude."
Kruszelnicki said he blamed himself for how things had turned out, and compared the Government to the scorpion that stabs the frog in one of the stories from Aesop's Fables.