Phil Hogan said the new PM was putting "the best interests of the Tory party ahead of the best interests of the UK" and had "stacked his cabinet with a ‘Hard Brexit Dream Team’".
The criticism of the nature of Mr Johnson's election comes after the prime minister described the Irish backstop as "undemocratic" in a letter to EU leaders.
But in apparent response to the claim, Mr Hogan said: "We should recall that the backstop was agreed by a prime minister who was democratically elected."
He added that the insistence that the backstop was undemocratic "seems strange" because it was "coming from an unelected prime minister" who had voted in favour of the Brexit deal in the Commons.
In speaking notes for the Commissioner's speech at a conference in Ireland, first reported by the Irish Independent, Mr Hogan is quoted as saying: "If the UK fails to prevent a crash-out Brexit they should be under no illusion regarding the foul atmosphere they will create with their EU partners and the serious consequences this will have for negotiating any future trade agreement.
"The UK continues to negotiate based on its experience of being an EU member. This misses the point completely: from the moment the UK came back to Brussels with the infamous red lines, the EU has negotiated on the basis of the UK opting for third country status."
"The UK government needs to take responsibility for its choices before it is too late. Prime Minister Johnson’s hero is Winston Churchill and he seems to view himself as a modern day Churchill.
"However, in the event of a no deal Brexit, the UK government’s only Churchilian legacy will be –‘never have so few done so much damage to so many’."
Mr Hogan has developed a reputation as the EU Commission's attack dog, having made a number of frank interventions in the Brexit process since talks began. In April he rubbished Theresa May's "global Britain" plan, warning that the UK would become a "medium-sized" nation with reduced bargaining power.
In June last year he said the tide was going out on the "high priests of Brexit", suggesting the British public were finally seeing through the “deception and lies” of politicians like Michael Gove and Nigel Farage.
His latests comments aimed at Boris Johnson come as former Tory minister Ed Vaizey accused the new [prime minister of being "hell-bent on getting no-deal".
Mr Vaizey said the prime minister was "going through the motions" in insisting that he wants the UK to leave the EU with an exit deal, warning that there was "no chance" of renegotiating the withdrawal agreement.
He told Radio 4's Today: "We're going to keep coming back to the Withdrawal Agreement, we're going to continue to have a hung parliament and a zombie parliament unless and until we leave the EU and parties can then campaign to try and get a majority.
"So we have to find a way to get parliament to agree to a deal and therefore I would give Boris Johnson the credit of at least forcing on parliament an existential crisis by being faced with a prime minister who is hell-bent on getting no-deal.
"He is completely serious about no-deal and there's no chance of him negotiating a deal with the EU, he knows that, he's just going though the motions."