The European Commission president said the bloc should not be held accountable for what is a “British decision”, stressing: "The European Union is not leaving the United Kingdom, the United Kingdom is leaving the European Union."
Speaking to Sky News’ Sophie Ridge, Mr Juncker said: “The EU is in no way responsible for any kind of consequences entailed by the Brexit.
“That's a British decision, a sovereign decision that we are respecting but don't try to charge the European Union with the responsibility.”
Mr Juncker hinted at concerns that a hard border in Ireland would lead to the return of unrest on the island of Ireland.
He confirmed that controls at the Irish border would have to be implemented if Britain were to leave the EU without a deal, insisting: “We have to make sure that the interests of the European Union and of the internal market will be preserved.”
But he said he did not like the prospect of a hard border, given the violent clashes seen during The Troubles.
The conflict between Northern Ireland and the Republic of Ireland lasted almost 30 years and cost the lives of more than 3,500 people, before the Good Friday Agreement
Mr Juncker told the Ridge on Sunday programme: "I don't like it, a hard border. Because after the Good Friday Agreement - and this (agreement) has to be respected in all its parts.
"The situation in Ireland has improved; we should not play with this.
"Sometimes I have the impression that some people are forgetting about the history.
“But history will be back immediately."
The Brussels official said he “was not criticising” British MPs and insisted he had “the highest respect possible for Westminster because it's the mother of all parliaments.”
But, he stressed, it was the UK Government’s responsibility to stop any Irish border from becoming “significantly harder”.
It comes days after Mr Juncker said he was “doing "everything” to help secure a withdrawal agreement because he felt a hard Brexit would be "catastrophic" for both sides.
"It's better for Britain and for the European Union to have an organised deal," he told Sky.
Simon Coveney discusses Brexit backstop agreement on Radio 4
He also suggested an openness to the contentious Irish backstop plans being scrapped, so long as they were replaced with a viable alternative.
Mr Juncker said on Thursday: "I don't have an erotic relation to the backstop.
"If the results are there, I don't care about the instrument.
"If the objectives are met, all of them, then we don't need the backstop.”