Addressing the European Parliament, Juncker said: "You will hardly be surprised to know that the Prime Minister assured us that he continues to want an agreement but, whatever happens, the UK will leave on October 31 with or without a deal.
"And that is why the risk of a no-deal is palpable," Juncker said, according to Efe news. He nonetheless described the encounter as "friendly, constructive and, in part, positive".
The Luxembourg politician also called on both sides to work diligently towards an agreement.
Juncker said the pursuit of a no-deal Brexit would never be taken by the EU but lay solely with the UK government.
With just 43 days until Brexit is scheduled to take place, failing any further extensions, Juncker said he did not believe "any real progress" had been achieved in finding a withdrawal deal that would work for both the EU and the UK.
The main sticking point, he said, was the Irish backstop, a mechanism in the withdrawal agreement designed to prevent a hard border between the Republic of Ireland and Northern Ireland.
Juncker said he had "no emotional attachment" to the backstop but that he stood by its objectives, which also seek to safeguard the interests of the Republic of Ireland, an EU member, and its cooperation with Northern Ireland, a UK territory.
He reiterated his call for Johnson to come forward with concrete alternatives.
The current withdrawal bill has been signed off by all EU members but was rejected three times by MPs in the House of Commons the UK's lower parliamentary chamber a logjam that led to the resignation of former Prime Minister Theresa May.
For hardline, pro-Brexit MPs, such as Johnson before he became the Prime Minister, the Irish backstop was seen as a capitulation to the EU.
Designed to be a kind of insurance policy in case the UK and EU fail to land a post-Brexit agreement, the Irish backstop could keep the UK in a form of customs union with Brussels until a deal is reached.
Johnson had held onto the option of a no-deal Brexit as leverage in the negotiations until opposition MPs wrested the parliamentary agenda from the government and passed a bill legally requiring him to instead request an extension in case he fails to secure his desired tweaks to the withdrawal agreement.
The Conservative Party leader's decision to suspend Parliament for five weeks ahead of Brexit seen by opposition MPs as a tactic to stifle Brexit debate is currently being scrutinized by the UK's Supreme Court.
( With inputs from IANS )